I don't know if you'll still touch this, but I do have to say, spectacular work! I pretty much use this mod 99% of the time I play the game, but there are still issues with it.
A few paths in some of the levels are broken from vanilla, namely in ACZ. In Act 2 for Sonic, there's a cave section after a half pipe and springs are supposed to launch you through the cave and Sonic will instead bonk his head on one of the wooden beams which isn't supposed to happen. Int the same act towards the end in the huge "underground" cliffside area, A red spring is supposed to allow Sonic to take a shortcut by landing on one of the large rock structures that leads to a secret, but it's impossible to reach.
Another thing is Amy's shortcut using the tornado in Act 1 is uncrossable.
I wish I didn't have these nitpicks, but things kept breaking as I used the mod. It's unfortunate cause the mod is REALLY good and I'm going to keep on using it.