1. Get the returns clean, spray a little carb clean or thinner. Can't really say oil there will hurt, but best not to, especially when trying to seal the end of the china wall
2. If the manifold sits right, rarely is there a hole alignment problem, however, the 4 end ones can sometimes be close. You can drill a little, but better to make it fit right with the correct gasket
3. I don't know what you mean on this one.
4. On the stand, drop it where you want it and turn the engine over with a ratchet, it'll drop. Then go back to TDC and check if you are where you want to be. In the car, use a ratchet or bump the starter.
It seems very odd the problems you are having. Can you take a picture of the manifold sitting with no gaskets and with the ones you propse to use?