He's got you covered on the window. The holes are for that stainless part that is along the back edge of the window.

The striker is an A body issue big time. Best thing to do is get the door adjusted so it is aligned properly WITHOUT the striker. Then make sure the striker is adjusted properly and the supporting metal will withstand the force.
This is where it gets tricky. They originally had a captured nut back there so the striker could be removed and installed. A body sheetmetal in this area is thin and it's commonly cracked around the captured area. So, you need to remove the Dr. quarter interior panel. This is so you can reach in and make sure of what is back there. It looks like it's been patched and painted. If so, you need to figure out what was done before you just go unscrewing the striker. It is quite possible that you will need to repair this area properly.
I don't go over to A bodys only forum, but I bet they have at least a dozen threads on this.