I need tips on cleaning an engine before painting

Modgod1

1974 Honda CB550 Cafe Racer in Progress
Ok got my 1974 cb550 engine out the frame, all the covers off (there being powder coated), then I used spray paint stripper. Tried lots of cleaning options, scotch pad, steel wool, sanding, dremmel, brushes, etc., but i still have some dirt mainly in between the fins, and around the spark plugs etc.

What's the best way to clean those areas? Also, am I correct in thinking, I should use denatured alcohol for the final cleaning before primer?

Last, I'm going to replace most the bolts when I've finished painting the engine, what I need to know is, do I leave the old bolts/screws/spark plugs in when painting, or should they be in half way, or out completely, and if so what do I fill the holes with when painting the engine?
 
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