B Devlin and some of the other guys that work auto body might want to chime in here too, but here's what I'd do...
You have a few choices and approaches depending on just how bad the clearcoat failure is;
...you can sand and block the roof with 400, then finally with 600 to 800 grit, feathering the areas (if there are any) of the clear that have broken through to basecoat. Then spray a high-build epoxy primer to fill in whatever uneveness is left. This should give you a decent footing for new paint, and you can sand /block the primer flat prior to painting.
If it's only in a small section of the roof ( I know in your case it's probably not), you can also wetsand the bad clear till it's feathered and has no transition edge from base to clear etc where it's broken through. You would feel those transition areas with with your fingers, you shouldn't feel a change in the level. Wetsand the rest of the roof with 800 grit, then blend some basecoat over only that bad area only, and reclear the entire roof. I did that on my wifus' red Miata driver's door (clear was flaking off top corner) recently, came out great. Just spot in the color only-reclear the entire panel.
Or....You could just strip it and start over from bare metal. You would still need to spray an epoxy primer though you wouldn't need a 'high-build' type. Just a bare metal primer &/or an epoxy primer/ sealer. In this case-scuff with 400 grit prior to painting. If it's as bad as you say, I'd go this route myself, you'll get the best results IMO and more peace of mind down the road, but's it's messy and a lot of work. Most good shops will do it this way, and perhaps your estimate reflects this method? Ask.
It really comes down to just how bad the clear is now. If it's flaking extensively etc. then it would likely be more work to sand it level enough to get it to where you wouldn't see the feathered edges etc. and get a flat finish, especially on black-because you'll see every slight imperfection in that.
If it's just in the beginning stages, and not lifting or peeling, you can probably just scuff it with 400 real good then repaint or at worst spray a primer/sealer/ surfacer and repaint. You only have to make sure the bond is good for what you're going to paint over, so you don't leave anything that's lifting or peeling, or about to.
B Devlin does it for a living, he might have better advice. I've only done a couple panels of clearcoat failure on other kinds of cars . Most all my paintwork experience is on cars that were stripped to metal, or scuffed oem paint in great shape( my SC for example). Mostly full repaints, not damage work. My wifus' car was the first blending work i've done.
But I think one of those routes should get you a nice roof again. You're sure in good company with Ford's lousy oem paint, the reasons for which I won't go into here.
P.S. One last thing; If you haven't painted before....think it over well. You may wind up regretting trying, there are a lot of problems a neophyte can run into, not to mention the materials' cost will likely be ~$100 to$150 for quality products, sandpaper, primers, base/clear. You'll need a decent spray gun and compressor. It all comes down to your experience with it and also your level of confidence. FWIW, I know there are shops that can do it for ~$250, so shop around and look at the work of a few of them, and ask about paint brands and warrantees. It may be worth an extra $100 over your material cost to have pros do it. For $400, make sure you're getting quality paint, because you should be. Best of luck Ken.
