1. Is there a way to toggle the Alt key function so that it's on all the time and items on the ground show up all the time (when they are within my characters perception range)? I really hate walking/running around having to hold down the alt key.
No. But you really shouldn't be holding down the alt button all the time. If you're in a cluttered room, use the alt button. If you just win a battle, use the alt button. If you "discover" something at random (via high perception), your character will notify you via dialog. There's absolutely no reason to hold the button down all the time.
2. Is there a way to force my character to run all the time?
Not yet, sadly. I agree--this is annoying. Hopefully they tweak the cursor-distance variables a bit. I don't remember it being as difficult to run in earlier stages of the beta.
3. Is there any known combinations of character classes that are just a downright plain bad idea to use together?
Just use common RPG-sense. IE think along the lines of party roles: you'll want someone who's good at ranged attacks, someone who can do area-of-effect, someone who can heal, someone who can tank, etc., etc.
4. For that matter, are there any just plain bad character classes that should be avoided?
Yes and no. It's a classless game--the "classes" you choose are really just starting ability/spell combinations. And, TBH, none of them are ideal. You can also replace spells/abilities at any time, so the main thing to keep in mind (at first) is to just pick a particular area to emphasize for each character.
IE don't try and focus on both melee and magic for the same character early on.
5. Is there an especially good character class combination that works really well together?
Yes. Magic-users. You may have noticed this about DOS, but elemental magic is a HUGE part of the combat system. And to fully take advantage of it, you'll need to be able to do spell combos. A spell combo is something like using a rain spell to do per-turn damage to a fire elemental by making it wet, and then taking advantage of its wet status & weakened status to do even more damage with an ice projectile.
You can do this with two party members, but I would strongly suggest just making one of your two heroes a magic specialist. Go for the Glass Cannon talent as soon as you can, which doubles your AP, and get at least 2 skill points in each of the four magic elements.