When I did my B4 headers (two different sets), I wire brushed and then steel wooled them as best I could. They weren't perfectly smooth. Not by a long shot but anything loose and any thing rough was removed. Then, I degreased them with something - paint thinner or something like that. Then I just followed the instructions on the can. On the stockers, to heat cycle them, I installed them and ran the engine in different increments. That lasted a solid two seasons before they started to look rough again. The V&H headers, I stuck in the oven.
I was REALLY pleased with the results both times.