Ok being a former RSS/RO player, and a FAR/AJE player now... I can say I think your problem is two fold.
1- Your engine is clipped into or through the bottom wing/heat shield this is causing it to heat up first. That and that engine has a lower heat tolerance than your craft. Check the max temp on that engine you maybe surprised.
2- Your craft is conducting a lot of heat to the engine which, as stated before has a lower heat tolerance than the rest of the craft. This is causing it to overheat then explode.
To fix this place some small radiators or some kind of intercooler between the engine and the craft. This or get a higher temp range engine.
EDIT- last thing.. the engine cfg file maybe messed up. Your temp range looks correct but it is overheating at a MUCH lower level than it should. 380k out of 2000k.
