Probably better in the SIB forum, but:
Probably OK to trailer with the motor mopunted, but I'd firm things up with a transom saver (though others will argue their usefulness, I'm sure.) Keeps the motor from penduluming while motoring down the highway. Some method of keeping it swinging lock to lock would be good as well.
I wouldn't worry about seams as long as you don't notice problems (peeling fabric, air leaks, etc.)
No clue on air vs wood floors; my SIB had aluminum. I'd guess that some form of protection (carpeting or the like) would mitigiate most of the damage dive gear would do.