Damn. You've covered all the common causes.
Other thoughts:
Motor mounts - I've read of some failing.
There are counterbalance weights in the crankcase - driven by chain - could that have broken?
How bad was the overheating you had? Did you lose coolant? Did gauge go into red? I'm thinking minor head gasket leak...
One or more injectors could be acting up - there's a "spray pattern" test that can be done - don't know what that costs...
Dunno...