You probably know I made published the 1-player TMNT2 TAS on this site. What you might not know is that I also wanted to make a 2-player TAS of TMNT2... but then I found the warping glitch which made a 2-player TAS for TMNT2 pointless (since you could idle 95% of the time with one turtle and still get the fastest result). I did however complete the first three levels of TMNT2 with 2 players (it obviously doesn't include the warping trick, since I stopped with this TAS after I discovered that).
Here is my 2-player TMNT2 TAS, which completes the first 3 levels (without warping).
Since you can't warp with TMNT3, making a 2-player TAS is certainly not pointless, and I would love to see it. Only real pointers I could give you is use frame advance, and pick a convenient button setup.
I know how frustrating making a 2-player TAS is, and even though I would love a 2-player TMNT3 TAS, I can understand if you are going to make a single player TAS.