I am trying to determine whether touch attacks benefit from modifiers. I understand touch attacks are versus the flat-footed AC of the target but it is not clear (at least as far as I can tell) whether touch attack rolls benefit from modifiers that a normal attack would use. For example, Ray of Frost (Core Rulebook, pg. 330) states it requires success on a "ranged touch attack." While that attack is done against the target's flat-footed AC does the caster get to add modifiers to his/her ranged touch attack roll? Dexterity? Intelligence?
First, it's not done against the flat-footed AC. Flat footed AC is AC minus Dex, and Dodge AC (and a few others).
Touch AC is AC minus armor and natural armor, but Dex and Dodge etc still apply (unless the target is flat footed as well)
Second, yes all modifiers to a normal attack still apply. It's a normal attack, the only difference is that it ignores the enemies armor.
Edit: Here's something on AC, and touch attacks: http://www.d20pfsrd.com/gamemastering/combat#TOC-Armor-Class