Just a heads up. I have played this hack for the last couple of days and found a few bugs, some good and passable but some requiring the use of AR codes and such. The good ones were just Rival May glitching out and always being (although invisible) in her battle spot on route 9/10, You have to re-battle her every time you pass through that gap (makes for easy exp but gets tedious when you have to heal at the Cerulean PC to progress to Rock Tunnel). Other bugs have been stated like the "body-switching" glitch, the known places for me were Celadon City with that trainer and 4 Island on the top-right hand corner of the 3-4 high stretch of ground parallel to the breeders. These bugs ion particular usually occur in menus when your character is "inactive" which may give some insight to the problem.
Also In Icefall Cave (also on 4 island) once you get up the Waterfall where Lorelei is meant to be, well, she isn't and although i'm fairly sure she isn't fully needed to progress it's something to look into.
Also, also, I am unable to battle the weather duo, Rayquaza yes, but the other two, no.
Also, Also, Also. In your General Changes document you have it put down as Shedinja gaining base 100 hp instead of the usual 1, which doesn't seem to happen in my game. On this subject of General Changes, most Pokemon I encounter that have had ability changes or additions will not spawn with their original, i.e. I bred a couple of Beldums and none of them ever had clear body. Similar thing with starters and never having their secondary ability.
I'm unsure if that's everything (foggy memory) but that's all I have for now.
Thankyou for this great Hack I much prefer the "minimalist" type hacks for these games, I dislike hacks that change way too much of the original game. As long as i can get most (if not all) and movesets are improved (Gen 3 has horrible movesets for most of my favourites) then i'm happy.