Based on what you've posted so far, I highly doubt it is a bur on the retainer or anything to do with the throw out bearing.
It does, however, sound very much like a heat soaked clutch cable that is in need of replacing. If it is fine when the engine is cold but acts up when it gets to normal operating temp., that instantly rules out a burr on the retainer. The burr wouldn't know if the car is hot or cold, it would act up all the time and most likely, after a few times of the throw out bearing rubbing over it (the burr), it would smooth itself out.
A worn out, heat soaked cable on the other hand, would act fine when everything is cold and act up when the motor was up to operating temp. The bas news is unless you address it, you run the risk of the cable breaking and leaving you stranded in whatever gear you happen to be in at the time and most likely, stuck on the side of the road waiting on a tow truck.
Based on what you told us so far, I would immediately replace the cable and see if that does it first, before I tried removing the transmission.
Richard
Tech Support
Tremec TKO, T45 & T56 Transmission Systems