Personally, that looks like just a couple of smaller holes. Depending on how far you want to take this fix, I'd blast the top to bare metal (or if you can't just use a wire wheel or something to that effect to clean it up), and go get some sheet metal at a hardware store and just patch those two small holes. Now, depending on how bad that pitting is (since I can't see it in person), if you're after replacing that whole front section, then yes a parts roof makes more sense. However, you said you're already planning on just smoothing it out with a little filler and treating the roof prior to putting another vinyl top on, so if the pitting isn't bad, I'd just clean up the roof, patch what's needed, smooth it out, treat the roof and proceed as planned.
2003 V-6 - the usual bolt-ons. Traded for 2012 V-6
2012 V-6 - premium "Pony Package" edition. Leased, so no mods. Traded up for 2013 5.0
2013 5.0 - premium package, visual mods for now.
1965 coupe - Born - straight six standard issue
Now - 5.0 motor, T5 tranny, R&P, full length subframe connectors, Caltracs draglink bars, hedman headers, disc brakes, MSD 6, paxton supercharger, and probably a bunch of other stuff I forgot to mention. It's loud as hell, and my new toy