Has the transmission been through recent maintenance/rebuild ? Could be improper assembly if so. Are you sure it has the correct fluid, and is filled to the overflow plug? I believe toploaders use old fashioned heavy gear
oil, not automatic transmission fluid like some newer transmissions. Is your driveshaft length correctly allowing for slippage of the output yoke, as the engine gets hot and grows rearward. Check for any other mechanical binding/interference under the tunnel. Like others who have commented, I have never heard of fluid getting that hot to cause a shifting problem. I don't think Shelby used trans coolers at LeMans. (someone will correct me if I am wrong) Sounds like something is binding due to thermal growth, either internal or external to the tranny. One last thought, are you running a hydraulic (internal) throwout bearing? Some have had problems with those. Good luck.