If it is all stock, then it would seem that the temp sensor is acting up. It is the little brass plug on the top of the head with a single wire going to it. If it thinks the engine is overheating it will shut it down. If you have deleted that thermal sensor, then it sounds more like a coil is failing under load. When it gets hot it starts to break down eventually not conducting through the secondary winding which is typically the way most coils die. If you are familiar with using a multimeter for electrical testing, place one test probe into one spark plug boot being sure to make good contact to the metal cap part inside, do the same with the other test probe on the other plug boot and see what the resistance values tell you. 3.5-4.7 k ohms is within normal range, anything above and your secondary winding is toast. To check the primary winding in the coil, you need to open up the e-box and test the two small wires leading off of the opposite side of the spark plug leads. The primary winding should read between 0.078 - 0.106 ohms.
Before you test for these values, be sure to zero your meter first. Touch the probes together and hold them there until you see the numbers stabilize. Most meters will read 0.3 ohms of resistance, this is the internal resistance of the meter. Whatever your coil test results are, minus whatever your meter told you when you checked your zero to get the true reading. Example, meter zero test reads 0.3 ohms, coil numbers on the meter read 100.3 ohms, the true reading is 100 ohms of coil resistance.
