I can't say for sure without seeing it myself but one of the biggest reason's an engine would do that is if the lsn was too lean. I know you mentioned you richened and leaned the engine but you didn't indicate which needles and in which order. The most common mistake among tuners is they run the hsn too rich and the lsn too lean. That is why you have engines that run great for the first few minutes and slowly develope lean bogs down low and eventually run into what we call ghost flames at the end of a straight. When the engine is on the hsn, with it too rich, it gets plenty of fuel but when you apply the brakes and close off the circuit and become lsn dependant, the lean setting dries out the mixture and the engine starves for fuel and flames out. The flywheel hitting the carb thing may be from times of chassis flex on big landings or if you the car dirt darts into the face of another jump so I can't sat for sure but I don't think the flywheel is hitting the carb at the exact moment you brake at the end of a straight. Not saying it isn't possible as I am not there to see this but I would look into other areas first. If you just can't seem to get it, send it in and I will run it myself and let you know what I find. Also a clutxh spring or bad bearing would also cause this but if it only does it at the end of the straights, unless something really weird is happening with the clutch, I will still lean towards the engine not being tuned correctly but again without seeing your engine and setup, I can't say for sure but it sounds like you have done the basic troubleshooting and all the signs of normal operation seem to be there other than your exact needle positioning.