I have a leveling mod that uses all skills to level up. It should have activated at the sewer exit [priority 0]. It is last in the list. I dried both in a patch and separate. Is it possible to use console commands to manually activate a mod the should started at the sewer exit?

That depends entirely upon how the mod is designed. If a QUEST record is not enabled at start and something is supposed to start it but failed, then you can use the console command "StartQuest" followed by the ID of the QUEST record. However if it is enabled at start and a script condition check runs to trigger it then you would need to check the script to see what the conditions are and then see whether you can use the console to set the conditions to match.

"...check the script to see what the conditions are..." I'm completely lost. So here it is [formid 01000ce7, standalone, bottom of list 4A]

scriptname SHAKEIautolevel

float fquestdelaytime

short shallwe
short menustage
short menuchoice

short levelreq
short statcap
short majoronly

short pluslevel
short newlevel
short newhealth
short newluck
short newstat

short plusagility
short plusendurance
short plusintelligence
short pluspersonality
short plusspeed
short plusstrength
short pluswillpower

short savedacrobatics
short savedalchemy
short savedalteration
short savedarmorer
short savedathletics
short savedblade
short savedblock
short savedblunt
short savedconjuration
short saveddestruction
short savedhandtohand
short savedheavyarmor
short savedillusion
short savedlightarmor
short savedmarksman
short savedmercantile
short savedmysticism
short savedrestoration
short savedsecurity
short savedsneak
short savedspeechcraft

short exacrobatics
short exalchemy
short exalteration
short exarmorer
short exathletics
short exblade
short exblock
short exblunt
short exconjuration
short exdestruction
short exhandtohand
short exheavyarmor
short exillusion
short exlightarmor
short exmarksman
short exmercantile
short exmysticism
short exrestoration
short exsecurity
short exsneak
short exspeechcraft

begin gamemode

if (shallwe == 3)
if (player.getav acrobatics > savedacrobatics)
set plusspeed to (plusspeed + 1)
set savedacrobatics to (savedacrobatics + 1)
if (exacrobatics != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav alchemy > savedalchemy)
set plusintelligence to (plusintelligence + 1)
set savedalchemy to (savedalchemy + 1)
if (exalchemy != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav alteration > savedalteration)
set pluswillpower to (pluswillpower + 1)
set savedalteration to (savedalteration + 1)
if (exalteration != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav armorer > savedarmorer)
set plusendurance to (plusendurance + 1)
set savedarmorer to (savedarmorer + 1)
if (exarmorer != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav athletics > savedathletics)
set plusspeed to (plusspeed + 1)
set savedathletics to (savedathletics + 1)
if (exathletics != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav blade > savedblade)
set plusstrength to (plusstrength + 1)
set savedblade to (savedblade + 1)
if (exblade != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav block > savedblock)
set plusendurance to (plusendurance + 1)
set savedblock to (savedblock + 1)
if (exblock != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav blunt > savedblunt)
set plusstrength to (plusstrength + 1)
set savedblunt to (savedblunt + 1)
if (exblunt != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav conjuration > savedconjuration)
set plusintelligence to (plusintelligence + 1)
set savedconjuration to (savedconjuration + 1)
if (exconjuration != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav destruction > saveddestruction)
set pluswillpower to (pluswillpower + 1)
set saveddestruction to (saveddestruction + 1)
if (exdestruction != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav handtohand > savedhandtohand)
set plusstrength to (plusstrength + 1)
set savedhandtohand to (savedhandtohand + 1)
if (exhandtohand != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav heavyarmor > savedheavyarmor)
set plusendurance to (plusendurance + 1)
set savedheavyarmor to (savedheavyarmor + 1)
if (exheavyarmor != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav illusion > savedillusion)
set pluspersonality to (pluspersonality + 1)
set savedillusion to (savedillusion + 1)
if (exillusion != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav lightarmor > savedlightarmor)
set plusspeed to (plusspeed + 1)
set savedlightarmor to (savedlightarmor + 1)
if (exlightarmor != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav marksman > savedmarksman)
set plusagility to (plusagility + 1)
set savedmarksman to (savedmarksman + 1)
if (exmarksman != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav mercantile > savedmercantile)
set pluspersonality to (pluspersonality + 1)
set savedmercantile to (savedmercantile + 1)
if (exmercantile != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav mysticism > savedmysticism)
set plusintelligence to (plusintelligence + 1)
set savedmysticism to (savedmysticism + 1)
if (exmysticism != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav restoration > savedrestoration)
set pluswillpower to (pluswillpower + 1)
set savedrestoration to (savedrestoration + 1)
if (exrestoration != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav security > savedsecurity)
set plusagility to (plusagility + 1)
set savedsecurity to (savedsecurity + 1)
if (exsecurity != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav sneak > savedsneak)
set plusagility to (plusagility + 1)
set savedsneak to (savedsneak + 1)
if (exsneak != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (player.getav speechcraft > savedspeechcraft)
set pluspersonality to (pluspersonality + 1)
set savedspeechcraft to (savedspeechcraft + 1)
if (exspeechcraft != 1)
set pluslevel to (pluslevel + 1)
endif
endif

if (plusagility >= 2 && player.getav agility < statcap)
set newstat to (player.getav agility + 1)
player.setav agility newstat
set plusagility to (plusagility - 2)
endif

if (plusendurance >= 2 && player.getav endurance < statcap)
set newstat to (player.getav endurance + 1)
player.setav endurance newstat
set newhealth to (((player.getav endurance)/10)*(player.getlevel - 1))
player.setav health newhealth
set plusendurance to (plusendurance - 2)
endif

if (plusintelligence >= 2 && player.getav intelligence < statcap)
set newstat to (player.getav intelligence + 1)
player.setav intelligence newstat
set plusintelligence to (plusintelligence - 2)
endif

if (pluspersonality >= 2 && player.getav personality < statcap)
set newstat to (player.getav personality + 1)
player.setav personality newstat
set pluspersonality to (pluspersonality - 2)
endif

if (plusspeed >= 2 && player.getav speed < statcap)
set newstat to (player.getav speed + 1)
player.setav speed newstat
set plusspeed to (plusspeed - 2)
endif

if (plusstrength >= 2 && player.getav strength < statcap)
set newstat to (player.getav strength + 1)
player.setav strength newstat
set plusstrength to (plusstrength - 2)
endif

if (pluswillpower >= 2 && player.getav willpower < statcap)
set newstat to (player.getav willpower + 1)
player.setav willpower newstat
set pluswillpower to (pluswillpower - 2)
endif

if (pluslevel >= levelreq)
set newlevel to (player.getlevel + 1)
player.setlevel newlevel
set newhealth to (((player.getav endurance)/10)*(player.getlevel - 1))
player.setav health newhealth
set newluck to ((player.getav agility + player.getav endurance + player.getav intelligence + player.getav personality + player.getav speed + player.getav strength + player.getav willpower)/7)
player.setav luck newluck
set pluslevel to (pluslevel - levelreq)
endif

RETURN
endif

if (getstage MQ01 >= 100 && shallwe == 0)
set fquestdelaytime to 1

if (menustage == 0 && player.getlevel == 1)
messagebox "Would you like to gain levels from all skill increases, or only from your major skills?" "Major only" "All skills"
set menustage to 1
elseif (menustage == 1)
set menuchoice to getbuttonpressed
if (menuchoice == -1)
RETURN
elseif (menuchoice == 0)
set majoronly to 1
set levelreq to 10
set menustage to 2
elseif (menuchoice == 1)
set majoronly to 0
set menustage to 2
endif
endif

if (menustage == 0 && player.getlevel > 1)
set menustage to 2
endif

if (menustage == 2)
messagebox "What would you like the attribute cap to be? (You should set it to 200 if you're using Legendary Mastery.)" "100" "200"
set menustage to 3
elseif (menustage == 3)
set menuchoice to getbuttonpressed
if (menuchoice == -1)
RETURN
elseif (menuchoice == 0)
set statcap to 100
set menustage to 4
elseif (menuchoice == 1)
set statcap to 200
set menustage to 4
endif
endif

if (menustage == 4 && majoronly == 0)
messagebox "How many skill gains do you want to be necessary for each level?" "10" "15" "20" "25"
set menustage to 5
elseif (menustage == 5)
set menuchoice to getbuttonpressed
if (menuchoice == -1)
RETURN
elseif (menuchoice == 0)
set levelreq to 10
set menustage to 6
elseif (menuchoice == 1)
set levelreq to 15
set menustage to 6
elseif (menuchoice == 2)
set levelreq to 20
set menustage to 6
elseif (menuchoice == 3)
set levelreq to 25
set menustage to 6
endif
endif

if (menustage == 4 && majoronly == 1)
set menustage to 6
endif

if (menustage == 6)
messagebox "Setup is finished. Enjoy the mod!" "OK"
set menustage to 7
elseif (menustage == 7)
set menuchoice to getbuttonpressed
if (menuchoice == -1)
RETURN
elseif (menuchoice == 0)
set menustage to 8
endif
endif

if (menustage == 8)
set shallwe to 1
endif

endif

if (shallwe == 1 && majoronly == 0)
set shallwe to 2
endif

if (shallwe == 1 && majoronly == 1) ;THIS IS GONNA svck
if (player.getav acrobatics < 25)
set exacrobatics to 1
endif

if (player.getav alchemy < 25)
set exalchemy to 1
endif

if (player.getav alteration < 25)
set exalteration to 1
endif

if (player.getav armorer < 25)
set exarmorer to 1
endif

if (player.getav athletics < 25)
set exathletics to 1
endif

if (player.getav blade < 25)
set exblade to 1
endif

if (player.getav block < 25)
set exblock to 1
endif

if (player.getav blunt < 25)
set exblunt to 1
endif

if (player.getav conjuration < 25)
set exconjuration to 1
endif
if (player.getav destruction < 25)
set exdestruction to 1
endif

if (player.getav handtohand < 25)
set exhandtohand to 1
endif

if (player.getav heavyarmor < 25)
set exheavyarmor to 1
endif

if (player.getav illusion < 25)
set exillusion to 1
endif

if (player.getav lightarmor < 25)
set exlightarmor to 1
endif

if (player.getav marksman < 25)
set exmarksman to 1
endif

if (player.getav mercantile < 25)
set exmercantile to 1
endif

if (player.getav mysticism < 25)
set exmysticism to 1
endif

if (player.getav restoration < 25)
set exrestoration to 1
endif

if (player.getav security < 25)
set exsecurity to 1
endif

if (player.getav sneak < 25)
set exsneak to 1
endif

if (player.getav speechcraft < 25)
set exspeechcraft to 1
endif

set shallwe to 2
endif

if (shallwe == 2)
set savedacrobatics to ((player.getav acrobatics)/5)
set savedacrobatics to (savedacrobatics * 5)
set savedalchemy to ((player.getav alchemy)/5)
set savedalchemy to (savedalchemy * 5)
set savedalteration to ((player.getav alteration)/5)
set savedalteration to (savedalteration * 5)
set savedarmorer to ((player.getav armorer)/5)
set savedarmorer to (savedarmorer * 5)
set savedathletics to ((player.getav athletics)/5)
set savedathletics to (savedathletics * 5)
set savedblade to ((player.getav blade)/5)
set savedblade to (savedblade * 5)
set savedblock to ((player.getav block)/5)
set savedblock to (savedblock * 5)
set savedblunt to ((player.getav blunt)/5)
set savedblunt to (savedblunt * 5)
set savedconjuration to ((player.getav conjuration)/5)
set savedconjuration to (savedconjuration * 5)
set saveddestruction to ((player.getav destruction)/5)
set saveddestruction to (saveddestruction * 5)
set savedhandtohand to ((player.getav handtohand)/5)
set savedhandtohand to (savedhandtohand * 5)
set savedheavyarmor to ((player.getav heavyarmor)/5)
set savedheavyarmor to (savedheavyarmor * 5)
set savedillusion to ((player.getav illusion)/5)
set savedillusion to (savedillusion * 5)
set savedlightarmor to ((player.getav lightarmor)/5)
set savedlightarmor to (savedlightarmor * 5)
set savedmarksman to ((player.getav marksman)/5)
set savedmarksman to (savedmarksman * 5)
set savedmercantile to ((player.getav mercantile)/5)
set savedmercantile to (savedmercantile * 5)
set savedmysticism to ((player.getav mysticism)/5)
set savedmysticism to (savedmysticism * 5)
set savedrestoration to ((player.getav restoration)/5)
set savedrestoration to (savedrestoration * 5)
set savedsecurity to ((player.getav security)/5)
set savedsecurity to (savedsecurity * 5)
set savedsneak to ((player.getav sneak)/5)
set savedsneak to (savedsneak * 5)
set savedspeechcraft to ((player.getav speechcraft)/5)
set savedspeechcraft to (savedspeechcraft * 5)

set newluck to ((player.getav agility + player.getav endurance + player.getav intelligence + player.getav personality + player.getav speed + player.getav strength + player.getav willpower)/7)
player.setav luck newluck

set shallwe to 3
endif

end

I'm not going to dedicate the time necessary to decipher that script. Ask the mod author.

Shake isn't around anymore. But I did noticed this line: (getstage MQ01 >= 100 && shallwe == 0). I used a mod that skips the red tape and starts at the exit. Main Quest stage probably didn't happen so, setting it manually might activate the mod.

Then the alternate start mod you used wasn't properly designed. It should have ensured that all variables from MQ01 and all quest stages were set to match as if they had been played through, as other quests and other mods may depend on this.