Gotta love durangos! We had one on a lease, it was 1999. My buddy had a 2000 like yours and it looked like this
Then..
Ok enough of the thread jack, looks sick so far!
Honestly, if you turned everything flat and the smell is still there it's up in the air what it could be.
Sub being warm could mean it's getting clipped or it's getting over powered.
I had a issue with a "rumble" and thumping when I switched songs and when I played a CD it was a nasty sound when it seeked. I grounded my RCA's to the HU it self and it fixed it.
Leave that bass boost off on both the amp and HU, unless you have a scope do not even attempt to use it. Check the amp output to the sub(s) and also check the voltage to the amp with the car on.