Personally I like to get the bare metal covered in epoxy primer before letting it sit. Now in your case, you have already protected the inside metal so any flash rust on the outside could be easily removed before continuing.

Yeah, I was kinda doing paint stripping while I was waiting for parts or other things working on the car, then like most was going to spray it all in once piece, 9 months later still in bare metal, but just about stripping all paint.

When you say "inside metal" are you referring to the wheel wells, floors and trunk? can flash rust rust through the metal, I kinda figured it was simply superficial rust that form from some moisture that gets on the metal? But yeah I have been using Master Series paints, a moisture cured urethane that is super resistant and strong finish, just have to finish the inside of the front fenders and start re-assembling that car. However, by garage is not temperature controlled and I dont see being able to paint in the winter as it is getting colder. I do want to do it myself, but have considered having a paint shop do the paint as I want to go with a Metallic, and I have heard it difficult to paint metallic correctly?

Thanks,
Devon

Yes, I noticed through your posts that you were painting the inner metal while doing your patches so it should be fine.
The surface rust will only be on exposed bare metal, if you get any at all, and will come right off.