A few more suggestions - all are related to upper valve train function.
Below about 3500 the VVEL is at minimum lift, after that it starts stepping up. For it to function correctly there has to be good oil pressure, which on our cars is over 100 psi. Also the crankshaft position sensor must be in perfect sync with the cam position sensor.
It is difficult to test the sensors when the problem is intermittent, but I think it would throw a code. If there was lower than needed oil pressure the ECU wouldn't throw a code because the oil pressure switch is set to 6 psi, basically to detect dry sump or oil pump catastrophic failure. If they are willing to hook up an oil pressure sensor and check the readings through the RPM range that would at least rule that out.
It also looks like you are bouncing off 3500 where as the normal over-temp limp program should soft-limit to 3500. This indicates to me that there is a malfunction at 3500 as opposed to ECU deliberately holding a 3500 limit. Worst case would be a partial blockage in one of the oil passages to the head, would show good oil pressure but almost impossible to diagnose. They would probably replace your engine before they figure that one out
