I painted mine with the engine in. I did't want to remove a perfectly running engine just to clean it up.
Mine is more of a driver than a show car and since it is the engine bay and prone to future grease, oil and scratches, I felt like it did not have to be perfect but be better than the original factory finish. Yours sounds like it is already at a good starting point.
Instead of a spray gun, I went to a automotive paint store and and had them mix my paint code (#240) in Acrylic and put it in a couple of Aerosol Spray cans. Much easier than getting a spray gun in there IMO. I could do the hard to reach spots like the battery tray area. You just have to be careful where the nozzle is aiming. Then I worked on one side at a time, cleaning, removing parts, and masking anything left Like AC hoses, wiring harness, etc. with masking tape and Paper shop towels. The trick with keeping it cleanable and shiny is to clear coat. It had to be compatible with the enamel. Got that at an Automotive store. The firewall was the hardest with the brake lines still attached. That is why I did one side at a time.
Overall, I'm happy with the results considering nothing major had to pulled. As a bonus, I even painted the visible parts of the engine block with ford blue using the same method, I keep an extra can of paint since there is always something to do under the hood and I can retouch or re-do something if needed.
I have posted before and after pictures on the AFM boot thread if you haven't seen them yet.