If your main caps are still installed w/ bolts rather than studs, I don't think there is anything you can do that will just bolt on to increase the bottom end reliability.

Not being a machinist, I'm curious why you need to have the main caps align honed when switching from bolts to studs, considering the caps fit into the main registers and the hardware is just there to strap 'em down. Yeah, I know, that's an over-simplified view... but still.