001: Agree, but again suggest the addition of rules for stopping drowning.
002: Hmm, a bit dubious. I think nearly everyone would agree that adding Invisible Spell to an Arcane Thesis'd Fireball should not give you a level 2 Fireball. However, not everyone would agree that Empower Spell + Invisible Spell should equal Empower Spell. I suggest splitting this into 002a and 002b to determine a more precise consensus, and would register my agreement to 002a ("A spell's level cannot be reduced below its original by any means of metamagic reduction." or similar), but abstain from 002b for now.
003: This seems reasonable enough, although I'd prefer limiting it to the problem class in question if possible.
004: Yeah, this should be fine.
005: Definitely, although a bit of rephrasing wouldn't hurt.

Rule 006: I Really Do Know Kung Fu!
Monks, as written, do not have proficiency with unarmed strikes. The first line of the monk's Weapon and Armor Proficiency feature should read as follows:
"Monks are proficient with club, crossbow (light or heavy), dagger, handaxe, javelin, kama, nunchaku, quarterstaff, sai, shuriken, siangham, sling, and unarmed strike."