your alignment does affect it. i'm not sure about any of this, but i think that anyone can be their alignment or Helm, and neutrals can choose any temple. I THINK that non-specialty clerics become specialty cleric kits in the process, if for some reason they weren't to begin with.
check out the
Universal Hint System for a help. it is the best hint site i have seen, and has some of the only data about strongholds. it also has a good way to only spoil you if you want it, unlike a walkthrough.