I struggled to just paint the dash panels. The primer and clear coat is easy, but getting the base coat (color) down was a total pain in the dick. I got base coat from 2 different vendors and had issues with both; wouldn't spray even.
Personally something as large as the entire roof and freedom panels........I would pay a shop to do it; unless you have experience in spraying waterborne paints.
Just an opinion here, but I think the chances of the two paint jobs matching would be a difficult task. Can I add another possibility? What about having the top sprayed with Line-X. I had this done with a 2010 Dodge Dakota that I still have. They have an upgraded Line-X (Xtra) product that provides an additional level of UV protection that doesn't fade over time. I had the front deer guard, and the side-steps sprayed, along with racing stripes up the hood, the roof, the bottom side panels, and a vertical stripe up the rear quarter panel. I still have the truck, and it hasn't faded at all. In fact, I still get a lot of compliments on it when I am getting fuel! I went with black, but you could also do a contrasting color (again, and this is only my suggestion, but I would go with something that was contrasting rather than trying to match the exact paint color). Kind of a nasty day here today, but I can go out and take some pics of it if you're interested.
I've thought about this, too. I haven't gotten a quote yet, but my idea was to simply have the top paint-matched and then cleared (no sanding it smooth or anything). I've also considered ordering a case of spray paint cans from the Jeep dealer and doing the same thing at home. I'm about to paint-match my faded cowl cover myself.