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I always just rub them with denatured alcohol and brush on Rustoleum. I have some that were done 3 years ago and still look as good as the day I did them. Others I have had to touch up after wrenching.
You can us a method that was used years ago on the Panheads to make the bolts black. They used to parkerize them to a black or dark grey finish. You can get kits and do it you self for around 20-30 bucks.
You might also look into using Hot Toppers for the bolt heads you want black. I am still up in the air over what I will do. I like the contrast of my Lo so I want all bolts on the black parts to be silver and all the bolts on the silver parts to be black.
I just bought a cheap can of satin Finish black heat resistant engine paint and painted all my grey bolt heads with that, they still look good after more than 2 years.
Did all the bolts that I wanted to black out with Testors Model paint. The Gloss and the Flat are really close matches for the HD Gloss and Denim black. It has held up very well and if I had to work on the bolts they touch up very easy. Less than a few bucks for the paint, brush and cleaner.