Is there a way to change some of the parts the gatekeeper has after the rebuilding the gatekeeper quest? Like via cheats or the construction set?

Uh you could modify him yourself. Theres no going back once you have built him

I don't have a save b4 and i was possibly thinking about changing his arm from an axe to mace just because the first gatekeeper had an axe arm and then the one your char. kills has a sword so... But otherwise ill probably just say screw it. The only way i think i can change it is via construction set i just wanted verification.

There's really no point in even thinking about the gatekeeper. His use is very limited to just a few petty Greater powers that you can only have one at a time.

If it's the look that you want to change, try going http://uesp.net/wiki/Shivering:Gatekeeper and copy down the BaseID that you want. Then in game, disable the current gatekeeper by opening the console, selecting the gatekeeper and type:

disable

Then type:

player.placeatme

Replace with the gatekeeper of your choice. Please note however, I doubt this will change the greater powers, and I may not even work properly, but give it a try.

Hope this helps.