I think the problems you are having with the clutch is from no front motor mount. Most people that put new motors in those cars don't put that motor mount back in because they don't think they need it, but you do. Without that motor mount you will feel a nasty chatter, shutter, clunking, and it will seem like it doesn't go into gear that easy. Check that motor mount and go from there.

But with the other problems what merf and everyone else said was right. Sometimes the wrong steeles are put in the car and the wheels don't mount up right so it could seem tight but it is sitting funny.