Dan,
I've worked at a few Ford dealerships and I am trying to remember what the code to the 3 stage could be. I know they had E9 which was lazer red tinted clearcoat, then they and another which was a 3 stage "bright red" code E8. My guess is that it is E8, especially since you didn't mention metallic in the two mixes.
Hopefully I am right. Most of the below pertains to that particular color code.
Some mixing systems make this a 2 stage color, and some systems make it a three stage. I would like to see you find a system that has a 2 stage. I believe PPG global was a 2 stage mix.
If you can...you might want to take the paints back (if they will, fat chance though) ,and see if they will find you a basecoat/clearcoat system that is a 2 stage mix.
This will make the process much easier, especially since you haven't tried the 3 stage paint before.
Whichever way you end up doing, be sure and use a
light gray sealer or base under the red. Reds are very transparent. It is very hard to get a dark spot covered. If you already have the dark gray sealer, possibly you can just spray a light bray basecoat. But you must use a light colored base or sealer.
*If* you do end up doing a three stage, use the light sealer for the spots, blend out the first base real good (Don't just try covering the spot and leaving it, you must blend this so it is nice a subtle, then you blend out the top color. Then of course, clear all. Tack in between coats, to keep the ends of the blends from getting grainy.
If you have spots real close together, you might as well, spray the light gray sealer and make it one big spot.
Also be sure and tack the complete panel(s) before clearing.
If you are flaming the panels, you can do this before you clear, be sure and get the flames done within 24 hours so you won't have an adhesion problem (or you can spray an adhesion promoter to take care of this). If you can't do this. Clear the panels, resand with 600 DA, then your good to go for the flames.
No hurry then.
Hope this helps you along!
Good Luck!!!!