[Enola Gaia]

Let's go back to the overheating incident ... How low on coolant were you? Did this happen while the outside temperature was hot?

Have you checked all the PCV and vacuum hose connections?

Have the timing, compression, and valve clearance been checked since all this started?

Have you confirmed your fuel pressure is within spec?

You didn't mention any checks made on the injectors. Have you verified all 6 injectors are un-fouled and working properly?

There are any of a number of electrical faults (shorts; bad connections) that could fake the ECM into running badly.

 

[Enola Gaia]

Those check engine codes, along with the rough idle make me think that MAF sensor is bad.

Good point ... Newby86 only mentioned cleaning it last year(?).