Have several issues with my game, and I am having difficulty pinning down the cause. Some of them are present even when all mods are removed, so evidently something is being put right in the save data

I have tried googling solutions to these already (its faster than waiting for someone to maybe feel like helping after however long on the forums after all) - but nope nada just a bunch of posts on crashes and such. My game doesn't crash, it is stable. It's just that some parts aren't firing correctly or other... oddities, are occuring.

TECHNICAL QUESTIONS: load order and designation

1) Is there an easier way to sort load order?

I'm enabling and disabling a lot of mods trying to find out sources of problems. However, Skyrim's inbuilt method is. The. WORST. It does not preserve load order - every time something is disabled, it is shoved to the bottom as well, into alphabetical order. Disable everything to test base game? HAVE FUN RE-ENABLING. Oh, you're doing that now? Oh look an update for one of your mods LET ME JUST ALPHABETISE EVERYTHING AGAIN. Alphabetical order is NOT automatically optimum order. Or we'd have dinner before lunch and put on trousers before underwear.

Tried just literally googling this, and nope, all the hits are "these are mods you like really need guys" or "what are mods" or "halp i has crashes".

2) If I have a reference ID for a problematic spawn (eg: duped NPC) how can I use that to determine the source?

As mentioned under problems I have duplicate NPCs all over Whiterun and don't know why. Their starter code is 69, so they are around the 110th mod based on hexidecimal. But I don't even have 69 in base 10, let alone base 16! That means I can't simply just count down the list to see what loads in the 69th place to see who thinks I want TWO ladies who won't shut up about how I can't stand the sight of strong women.

SPECIFIC PROBLEMS: do you recognise either?

1) COMPANIONS DO NOT OFFER LYCANTHROPY. (All saves.)

Proving Honour: Vilkas does not wait outside. It is possible to skip him. Alternatively, I can walk around to wherever his route normally takes him and talk to him mnaully.

The Silver Hand: Never starts, EVEN WITH CONSOLE COMMANDS. With all mods disabled Skjor says "there you are, wanted to talk to you" but quest will only start with console commands (setstage C03 5).

I do not have any mods that change the Companions, so I have NO idea what's happening there.

2) MULTIPLE DUPLICATE NPCS

Eorlund Grey-Mane being one I remember the name of. Quite a few of the Battleborns and Grey-Manes. The code at the start on the dupes was 69 (later 68) which in hexidecimal would make it about 110. I DON'T HAVE THIS MANY MODS, so I don't know how to find out which is spawning them!

A messed up mod mix will do bork your save in many ways, and removing the mod does not remove the problem that is now in your saves. Mostly it's script related. Remember, your not adding content, your recoding the game when adding a mod.

As for sorting mods, BOSS is the program for that. Then there are other programs like Wrye Mash (Bash? I never keep up with the names) to take care of mod conflicts.

Then, once you get your mod mix sorted and working together, then you will want to load a save from either before you added any mods, or maybe just start a new character.

1) Because as you say, the default launcher is woefully inadequate when it comes to sorting above a dozen mods, that's why many people end up having to use at least one of the third party mod organizers.

That said, I highly recommend http://skyrim.nexusmods.com/mods/1334/? especially if you want to test different mod combinations. It allows you to save multiple mod profiles, easily disable/enable whichever mod, and clearly see what is overwriting which mod in order to detect conflicts. It does this without affecting your actual Data folder, which is the main draw. Meaning that you will always have a clean main Data folder, with the different mods all placed neatly in their own folders due to the method MO uses to load your mods.

There is also a http://skyrim.nexusmods.com/mods/31499/? available to help you get started.

It can also sort the mods in your load order with BOSS and you can use other tools like Tes5edit and Wrye Bash through it as well. The guide will explain how to do it.