1) My hood scoop is the same way. It has a gap about 3 inches from the tip back, then it settles flush with the hood itself. I pisses me off but I don't plan on messing with it. I'll probably bring it to my body shop and have them take if off and re-glue it with automotive adhesive.
2) You could check the clips to see if one is broken...be careful if you take it off, sometimes the clips break upon removal
You could probably glue them to the car as well. Again, I'd check with your paint guy or body shop for suggestions on adhesive.
3) Yah, unbolt those small screws on the inside of the fender and move it around. I had to do it when I got my GT hood. Just make sure the gap is even between the fender/door and fender/front bumper. This make take a couple of tries to get just right. Also don't forget to screw the bolts back in all the way, lol.
4) I'm trying to picture what part you're talking about. My guess would be to replace that bolt. It's a good idea to have missing bolts and parts like that replaced.
You could replace the driver skin. They are expensive new. You could try and find a clean one off a wrecked car and have it painted.
If you have the dual exhaust tips out back, I'd get the GT bumper. It really improves the look of the exhaust with the 2 cutouts. Plus, you can't beat $100 to paint the bumper. Silver is a pretty popular color, you might be able to find one for cheap already done up.
I've heard that the cobra bumper is different than the v6/GT/99-01 cobra bumpers. I think it may have issues with the regular hoods like the GT hood. I'm not sure about shaving the top posts around the grille area. Maybe someone will chime in about that. Iirc, jimmy_beaner had the 03 cobra bumper with the cobra R hood and he had issues with it lining up. I don't think he had issues with the hood closing all the way though.