I have had good luck with Plasti-Kote Hi-Temp paint for headers. They claim it's good to 1500F. As Wick said, be sure to follow the directions and heat cure the paint.
DON'T mess with the inside of the header flange. That roughness that you're worried about will help the gasket seal and keep it from moving around.
250/292 heads came with two locating pins. One on each end. Inboard of each of those is a threaded stud with a fine thread nut. All the other manifold fasteners were bolts. The pins are threaded in and can be removed. Replace those and all the bolts with studs. Your head may not have the studs, because the head rebuilders like to take them out and not replace. Of the original clamps, some are long and some short. With the Clifford intake, I used six short clamps and a total of eight studs.
The header flanges are not very thick and will warp easily and leak. DO NOT OVER TIGHTEN THE NUTS.
Most people here will tell you to get a Felpro header gasket. I recommend the cheapest one piece header gasket you can find. Just like the ones you have pictured. I tried a $30 felpro and it lasted one week. What ever gasket you choose, do NOT over tighten it. It will leak for sure.
Holding the two header pieces, the gasket, and the intake against the engine and starting the bolts is a juggling act. The studs make the assembly very easy and helps with the gasket sealing.
The box and gaskets should not have been damaged, but I don't see a problem with the rest of it. If you had put out the money for ceramic coated and got that quality of finish then I could see your dissatisfaction.
