1. I just lay it over them, and as soon as I lay it over I use a razor and just trim around it.
2. It is recomended to cover those holes, there are a couple of different ways to go about doing it. You can get a piece of tin or thick aluminum and cut to the shape of the hole. Cut it a little bigger than the actual hole. Cover one side of it with raammat then place it over the hole on top of the already matted door. That way you don't have metal against metal, rather two layers of mat against each other. Then cover the piece with raammat so that you overlap the tin piece with raammat. It might be a good idea to use some liquid nails or caulking glue between the tin peice and the door for added measure.
3.Before lying the mat down identify all screw holes and either work around them, or remember where they were right after you lay down the mat and cut away the mat for the holes.
4. I used diluted simple green with good results, just remember to wipe it with a wet rag after using the simple green. You don't have to worry too much about the tar that's there from the plastic barrier, just mat over it, take off the big chunks.
5. Yes, definitely.
You really ought to look into some ensolite foam or volara foam off ebay. It will cut down on the road noise. The raammat is mostly for stopping panel rattles.
Here's another good info thread.
http://www.diymobileaudio.com/forum/viewtopic.php?t=29