Well, you could put something over the crank to protect it during the process, then turn the engine back over to clean everything out (that way it runs away from the crank). There honestly shouldn't be that much junk coming out from honing. You're just scratching the surface.
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'13 Mustang 3.7V6 - MT82
'00 GP SE (L67 Swap, XP, Headers, 3.25")
'98 GTP, '01 Bonne