The 3 hole cover was likely for the alternator cover, though it may be for the CB500/550 if the fins don't angle right. The clutch cover does have to be cut away, or the kickstart won't fold in at all.
Racecrafters was an icon on the Sunset Strip in Hollywood, one of the first shops to specialize in cafe racer and racing parts in the late '60s. They originated those finned engine covers, along with the ubiquitous clamp-on-the-the-fork-tubes 3 hole headlight brackets. George Kerker distributed his 4-into-1 exhaust solely through Racecrafters, and they sold Yoshimura parts, when it was still Pops Yoshimura.