A clean install means you create a new partition and in the lion install screen go to disk utility and unmount your old lion install or completely wipe your old lion partition. You cannot have any lion install mounted anywhere on your drive while installing lion. it pulls stuff from the other partition when installing.
also my problem is not caused by overheating. my problem results in overheating from kernel_task using 100% of the cpu. the cpu is never "throttled down" due to heat. If it gets hot it turns the fans on and if the fans cant keep it cool it will hit ~100°C and shutdown.
The closest answer I can come up with is that when you upgrade from snow leopard or lion the kernel or some of the kernel's dependencies gets corrupted causing it to enter an endless loop which can only be exited by unplugging either the mini-dp or power. This is likely code dealing with the ability to use a second display, keyboard, and mouse with the lid closed.
In any case try backing everything up(SuperDuper is awesome) to any external drive and completely wiping your drive to reinstall lion from a flash drive/dvd(apple has now posted a utility to create bootable rescue media or google it, there are plenty of guides or utilities.) Make sure to have your external backup unplguged when installing.
