Another update: I've found a way of syncing the audio - Playing the movie from the beginning each time I change something. Joy.

Ah well it's better than not being able to sync it at all.
EDIT:
I've uploaded what I've got so far, bear in mind that
some shots are still temporary (
especially the first shot of the factory front), there are still some syncing issues (I'll silence the pistons during the barrel scenes to make it much less noticeable), some shots will have to be re-done (like the prison cell scenes and Molluck). There are a few errors too that I'll have to get rid of. Other than that it's looking very good - But it needs to be polished to a mirror shine.
Preview 1
Preview 2
Suggestions and feedback welcome! But bear in mind that I'm probably already aware of what you may highlight.