M'kay, how about this instead:
Adapt the first three issues in the order 2-3-1.
- Baxter builds MOUSERS and betrays April
- Turtles rescue her and the origin is told.
- Reveal that Baxter did the MOUSER stuff for the Foot clan because they wanted funds and that he is the key to get to them.
- At this point the whole car chase happens, replace the police with the Foot or MOUSERs.
- Turtles get to Shredder and kick his ass, pretty much the end.
- Optional, end with the cliffhanger of Splinter having gone missing and he wakes up in an Utrom lab.
That's pretty much the skeleton of the story and obviously there needs to be additional details, but it really doesn't need to be much more complicated than that. Set up the basics, have some action in the middle, end with the big bad being defeated and maybe add a cliffhanger depending on wheter or not you want to make more.