I don't know of any close by Allison shops, is this something a dealership can usually do?
hot flushes are becoming more common in transmission shops. it heats the oil to a desired temp, then forces fluid through the lines i think around 100PSI, then at certain timed intervals, it hammers fluid in the reverse direction for a split second and then goes back to flow. that knocks shit out of the fins and caught areas while the hot fluid expands everything like jason said.
it does one hell of a job of cleaning things up.
if you cant find one, pull the lower trans line to the radiator and post a pic up of what it looks like inside the radiator. might be better off just buying a new rad. Then drop your trans pan and pull the internal filter, split it and open up the media. then put a pic of that up. we can see how much trash has gone through the trans then.