Here are a couple of suggestions:
- Trim the scenes of April and Casey in custody, remove entirely if possible.
- Remove the dick and fart jokes.
- Remove the explaination of Bebop and Rocksteady's mutation, none is better than what we got.
- Remove the "we could be human" plotline, it went nowhere.
- Add a text crawl or something explaining some of the unclear things, like who or what Krang is. You could add a new explaination for how the mutation worked.
And if there are deleted scenes that fixes any of this, please reinsert them.
I must admit, it's a good idea to start with the transfer scene.