Help patching small spots on my 100

[KBrummer-KY]

I have 2 spots on the roof of my 100 where the wind guard screws were tightened every time the shield would warp. Eventually they touched metal and scrached the hell out of the roof. When I bought it and discovered it, it was too late. Here's my plan:

I bought the stuff that is supposed to turn rust to a hard black "primer" and neurtalizes the metal/rust. (I'll get the name of it when I get home) I plan to sand out all rust (how far should I extend past the rust) and apply this neutralizer. Once done, I will apply OEM touch up paint. The size of the spots now are showing about 1/2 inch. Looks aren't as important since it's on top of the rig.

Last, I noticed in the wheel well where the plastic meets the back of the fender, theres some rust. It seems to be on the edge of two pieces of metal coming together. Should I use a different technique on this?

I'll upload photos ASAP.
FYI, I am totally new at body work, so give it to me straight up!

Thanks,
Kevin