I'll tell you what Ripped, I have done MANY of those Mustangs and if this car is painted apart, I highly recommend bolting the fender and quarter extensions on as I suggested when it is painted. I have a co-worker with a pretty nice 67 GT fastback at the shop right now, paint looks pretty nice and those darn quarter extensions are a different color!
Fenders and doors are one thing, but then the painter turns around to paint those little pieces it is VERY easy for him to apply the paint differently and they end up looking different. YES, it is possible to do it right, but bolting them on with some washers behind to space them away from the body gives you the exact same result as painting them off the car but with a perfect exact application of paint. It just makes sense to me.
From what I have learned about you, your skills and your expectations, I say jamb the car and bolt it together to paint it. The biggest thing about doing this is that it is masked well in the jambs and that nothing is going to be applied but paint and clear. Lets face it, if you were to have gotten this car and it was fully restored, with only the paint on the outside faded. Let's just say that was the case, the paint was simply faded real bad and wouldn't polish. The jambs were all perfect in the color you wanted, you most likely wouldn't have pulled all the panels off to repaint them, am I right?
I am not telling you, I am asking you to look at it that way. If you would have done that, maybe that is the best choice now.
Painting it apart is ALWAYS going to be the "best" way to do it, but whether it is the "Bestest" way for YOU is another thing.