I've been thinking about this one.

The running with the idiot lights on is strange.

I would suggest unhooking any and all aftermarket stereo stuff. Then double check all the ground wires. There are a couple behind the head at the firewall (One off the valve cover, one from the the head and one behind the bracket for the EGR pipe. They tie into the firewall at a little clip in about the middle.).

There is also a ground wire for the ECU. Since it has been replaced, I am wondering if it got missed.

The lights are somewhat suggestive of an electrical problem, somewhere.

Good Luck,
Michael

PS, the next option is to pull codes from the ECU an see if they might be helpful.