Agreed with above, If it is farely clean I used a scotch Brite to scuff it up before paint.
Might not be as bad if I do that after trying to remove as much as possible with brake cleaner.Messy as all get out, but use a small wire wheel on the drill where you can
No, I didn't do anything with the water passages. All of the antifreeze that has drained out has been bright green so I figure they're clean. I have not seen the windage tray you are describing.

My headers don't leak. I've never been without a vehicle with headers. Don't waste time or money on gaskets made of anything less than aluminum or copper.I'm honestly not a huge fan of headers but I'm trying to pick up power where I can. Also the exhaust manifolds on the motor now need replaced. I do know from experience with the 71 cuda we owned that ceramic headers are far superior to uncoated.