So, now that the car runs enough to drive it up onto the trailer, it's time to start doing some body work. At the minimum (as long as I don't find any huge trouble spots) I'm looking at replacing the entire floors (trunk unknown), most likely the cowls, a 2-square-inch spot on the passenger fender, and a small corner on the passenger door. After, I'll probably be spraying my own primer, and MAYBE painting. I have someone willing to do the welding and patching work for me very cheap or free (retired, and just an awesome guy).

Obviously I'll be pulling the fender, and possibly the door, off to do the patching. My question is, would it be smartest to sand and primer it while it's off, or just get the outside when it's bolted back on? Every painting guide I've seen has either shown stripping the car down to nothing (the best, but most tedious way), or primering / painting with the body panels still bolted on. Should the inside of fenders get painted, or just primered, or something else?

Also, I need to replace an inner fender well on the passenger side - the part that holds the battery box. Other than that being rotted, the engine compartment is dirty, but doesn't look that bad. Does the engine compartment usually get painted, or sprayed with high-heat paint? I'm not worried about it looking perfect, but I don't want a bunch of painted black sheetmetal, and one brand new shiney (soon to be rusted) piece.

Finally, the car I have is a '66 Coupe. I'm thinking of painting it Sapphire Blue (only available on the GT350s for that year, I believe), with white LeMans stripes. In your personal opinion, does that sound lame? The rest of the body will be stock.

 

This is my opinion and advice to you, but it is just that.....my opinion. You can learn from it, or you can ignore it.
Racing stripes were designed back in the day when cars made a lot of smoke and ran on dirt tracks, so the blue stripes on a white Shelby GT350 pointed the driver in the right direction. They were not a trademark or a cool thing to add. There was a real reason for them. Now, Shelby put those on his GT350's which were fastbacks, not coupes. Putting racing stripes on a 65 Mustang coupe would be like putting racing stripes on a Geo.
You are correct in that the Sapphire blue was a Shelby color. However, in my opinion the darker Acapulco blue would be a better choice if you are not going to put racing stripes on that coupe.

 

The strips is an idea I was toying with, not really sure about. I actually thought it might be lame on a coupe (if it was a fastback, no one would be able to talk me out of it...), but I'm not sure.

I saw someone else that had stripes on a coupe - it didn't look horrible, but not as awesome either. To me, it adds character to the car. I just don't want Mustang enthusiasts or any of the older crowd telling me I ruined the car or tried to make something it's not.

Either way, those are a long way off. The body repair is first, and paint is at least a month or two away. I appreciate the opinion though.

Do you have a link to that paint? I can't find any of my old paint charts for 60s Mustangs.