For the train racing scene, did you try making the motion blur a bit more cartoony and colorful (like Smallville)? Still, I thought what you did worked well.
I don't know what the complaint is about the missile launch. I thought the scene flowed fine.
Have you considered not joining the two films directly but putting in an intermission card and running the score for a minute or two? At that runtime, it's not unreasonable.
Of course you could just make it a 2-disc set with the disc change covering the problem. 2 DVD5s are cheaper to burn than a DVD9.