Well - i got the job done. In the end, I used a brass wire wheel to remove all the crap. I spoke to an aircraft painter. He said they always take the seals off and paint the door first but only for astectics. They acid etch then alodyne and prime. For small areas, he said they prime with a special etch / primer. Anyway, i covered all the bare aluminum with the 3M adhesivive that the door seal people recommended. After applying the seal, you cant see any of the unpainted area anyway.
Got the seals from Aircraftdoorseal.com. They were helpful and said often, with really old installations, they use the wire wheel as well. The seals good, but in some areas are too wide for the door and I had to trim. They definately don't look as good after trimming. The doors are pretty tight to close now - passenger side was really hard, but they should wear in eventually. For the money ($400
), not sure I'd go this route again.
It was a good learning experience tho. Also got my new Sporty's air vents in, my 150 lb upgross and the oil changed so all in all, was a productive 2 days of work.