One thing I've done to minimise the total slop is to drill all clearance holes to minimal size and then enlarge as required. It's a tedious process and you will need to decide whether it's worth it considering the amount of repeated assembly/disassembly required.

Wherever possible try to design in a way that you can adjust only one parameter at a time and not have to undo one adjustment to get at another. That's much easier said than done.