cleaning the rods

should you tap the bolt holes on the rods as well ? just to be safe

With a new set of aftermarket rods this generally isn't necessary. It's not a bad idea for rods that are a little older and have endured several tear downs and rebuilds though as this is when dirt, debris and general crud are likely to gather. Likewise if you ever have difficulty installing a rod bolt by hand where the bolt isn't free to turn then this would also suggest you have some potential problems with the threads.