It was indeed the RDU Coupler. No more thumping on normal acceleration, but under heavy WOT it will do a slight thump. I think that has to do with the fact that there was no code on the unit to update the PCM with, but I am not getting any CEL or wrench ( at least not since I plugged it in after forgetting to).
What I thought was the code, turned out not to be, but its already installed, not much I can do about it and it works.
What I thought was the code, turned out not to be, but its already installed, not much I can do about it and it works.