Parts not showing correctly

Its very hard to say from that picture. What exactly did you do to the model after importing it? If you explained step by step then perhaps I'd be able to help you, but I can't unless I know exactly what you're doing wrong.

This actually looks similar to a problem I had once, when the hi.yft and the normal .yft file came from two different models. Have you exported both of those files in ZModeler (the hi.yft needs to have the L0 only, the normal .yft L1-L4) and added both to the game?