The flushing machine that passes down the fill tube simply removes oil passes it through a filter and returns it at the same time. I don't think that'll help you.
You could drop the pan and use compressed air but that could push the problem deeper. Best way I can think of is to drop the valve body and carefully remove each valve and use a magnet to try and grab / remove anything floating around. Then flush clean that port, re-assemble that valve and move on to the next one. Or as my dentist likes to say, "rinse and repeat".

This should have been performed during "the rebuild". Like the C-4, the valve body needs to be torqued in the proper sequence also, do it wrong and the VB will twist and never shift right after that. You can get the torque settings and sequence from a Chiltons manual or maybe even youtube?

I'd be tempted to say leave it alone and maybe it'll clear itself but sometimes the noise is worse than the fix.