Ahhh!

Not been introduced to Zoids yet but that definitely sounds like a great project!

The best for us to give you advice is to put pictures up and ask specifics depending on what you wish to do.

But as a general advice on restoration, since you mentioned broken and missing parts, you would like to give a try on casting (by molds) or creating (no molds) your own parts, this is done with an epoxy called "green stuff" (and don't buy Citadel's green stuff, theirs is way too expensive), you would also need a sculpting tool set.

However, if your models have paint, the first thing to do is to strip the paint; then you continue to take all pieces apart if the parts that you glued on look horrible, this will allow you to put the pieces back on the right position if necessary; after this, you repair or reconstruct partial or complete parts with the "green stuff" followed by sanding to make all pieces as smooth as they need to be; then goes priming, painting, weathering.

This is just a broad overview of how restoration takes place and what is on the top of my mind at the moment.

If you got any questions, let me know, I will be glad to help out! 

Luis