F*ckin A I figured it out. FINALLY. Went a bit mad getting to the bottom of this, but.
So here's what everyone needs to do to start cranking out their own voicepacks or sound effect mods:

-Get the mod API from the TMNT SR Nexus and install it
-Get the SoundExtractor also from the Nexus, use it to unpack your SFXPack.pbn
-It will unpack everything to a folder called "Extracted". Take the "Audio" folder from out of that and move it to the base game's "Content" folder. You can now delete the "Extracted" folder. It served its purpose. (unless you would also like to mod the menu select sound effects, then move that folder too.)
-Now is where you get your wavs you want to replace stuff with.

The only wav encoding this game will agree with are the following settings:

bit rate: 1 536 kb/s
format: PCM
format settings: Little/Signed
bit rate mode: Constant
channel(s): 2 channel stereo
sample rate: 48.0 kHz (48000)
bit depth: 16 bit
stream size: 416 KiB

the only program I have that is able to go up to a 48000 kHz sample rate is my Magix Music Maker program, but I would imagine perhaps newer versions of Format Factory or Audacity might have that reach too? Magix is intended for recording actual music, kind of like FL Studio. So FL Studio is also a thought. You're all smart people, you probably have some good programs already. But anyways there it is. Once your wav is encoded as stated above, just rename the file to what you want to replace, like "Ennemy_Hit.wav" and overwrite as par for the course. Bear in mind your volume levels - this games music and sound files were quite amplified. So you want to raise your levels, just don't go in the red zone too hard with it.

REMINDER to ignore "Mod options" in your TMNT main menu in-game (an API thing), it will crash the game. Its useless to us anyways, act like it isn't even there. Mod API isn't updated, but it works enough to allow us to do this. Without it, there's no way.

Now lets get making some harder battle sfx and make Casey Jones sound like Duke Nukem