First, how exactly is XP distributed between party members? After playing for awhile, I noticed that all my characters have slightly different XP totals. Is this related to class, stats, etc?
It's been a while since I played MM6, but I seem to recall a skill called Learning that affects XP gain. Other than that I think it should be equal. Maybe being dead has an effect.
About Perception.. I know secret doors, etc. will turn red if someone in my party has high enough Perception to detect them, but is it still possible to use those things even if they're not detected? i.e. Can I open a secret door by clicking on that area if it's not detected?
No.
What are generally considered the "must have" skills to start with? I already regret not having Identify or Disarm Trap in my party.
I also like having Repair, Perception and Alchemy. The latter is optional.
My only complaint is that there seems to be very little penalty for a party member getting killed. Only 20 gold per level to resurrect them, and completely restore hit and spell points?
I believe that depends on where you do it. In New Sorpigal the temple is very cheap.