Clear Coat Parts, Replacing screws with Stainless, Painting

I posted these questions on the K100 forum. I haven't heard anything back (it's only been a few minutes) but I thought there might be other readers that could comment.

Although the cosmetics aren't my primary concern at this point, getting the bike running is, I'll be tackling the finish later on. But while taking the bike apart to get to suspect parts I'm removing some components.

The battery tray. I've removed it, one of the grommets won't come out and I've done some polishing. It's aluminum. Should I put a clear coat on it to keep it from staining?

One of the things I'm wondering about is the screws that hold a bracket/rail on the sides of the throttle body. This is the bracket that holds the throttle stop on the outside of the bike, on the interior side of the bike it holds the fuel pressure regulator and what looks like a pressure switch (i can send photos). Many of the screws are a bit rusty, some have corrosion. I've removed them singly, because I don't know if they hold anything on the inside of the rail/bracket, and polished them to get the rust off. Can these be treated with anything to keep them from rusting again, wax, clear coat, although I don't want to fill the phillips heads. I tried to find new screws (non BMW). I found some M4/10 SS screws, they are shorter than the bmw screws probably 1-2 mm's shorter. Has anyone replaced these with Stainless screws? In boating we worry about the corrosion on dissimilar metals, stainless into aluminum. We used to use Boshield T4 (I think, it's been a long time) this was said to prevent gulling, the electrical corrosion between the metals.

The question of different metals is one that I'm wondering about. I wouldn't mind replacing most anything that is rusting with SS screws. It seems to me so far that where screws are used they are typically on non bearing or load applications. SS Replacement shouldn't cause a problem, should it?

I removed the fuel rail to to test and clean the injectors. I cleaned the rust from some spots on the rail. I bought some black Rustoleum engine paint. I also got some primer. Unfortunately, I didn't notice that this was not engine paint do you think I'll have a problem? I used the primer 3 coats sanding. Black paint 2 coats, sand, third coat.

I'm going to try to post pics here, I haven't figured out how to post them in the K100 site.