As I'm understanding it, RAY spells act like Ranged Weapons, so I get cover and firing into melee penalties when trying to shoot someone..
What about missile type spells, like Acid Splash or Acid Arrow?
Does it apply to all ranged touch attacks?
If so, is there any way to get around this?
Precise Shot only seems to work with Ranged Weapons, but I don't see where it says missiles or other spells are considered 'ranged weapons', only ray spells.
Just could use some assistance understanding this better. I was suffering from -8 because of cover and firing into melee for most of my first battle with my wizard (lvl 4) and couldn't move around much because of confined space.
Yes, rays need a ranged touch attack and you are penalised:
-4 for firing into melee (Precise Shot feat needed to counter this, needs Point Blank Shot first);
-4 for any cover, or -8 for improved cover (Improved Precise Shot, needs BAB of +11 as well as the previous feats).
Acid Arrow quotes: "You must succeed on a ranged touch attack to hit your target", so yes, you must succeed on a ranged touch attack to hit your target.
As far as I know, Precise Shot and other feats apply to spells that require ranged touch attacks, but I can't find the actual reference at the moment.
However, it is rare that it's worthwhile to take those feats as a wizard - the 'touch' part of the attack means that you're likely to hit most enemies anyway, except when they get cover against you. Train your party members to let you fire your ray before they charge into melee, or train yourself to use other spells when you can't hit the enemy!
If there's a attack roll at range, then cover applies.