Elm327 was the cause. Wouldn't have ever considered that.
Next week it's going on to a hoist and getting Transmission service and PTU looked at. Hoping it's the cause of my noise.
I'm back at square one with it. We've more or less ruled out the motor as there's no drop in power when sound occurs.
So far it occurs more often on hills than flat road, is barely audiable on flat road actually. I've had success making it occur while accelerating where before it only occured after a shift. Still a hit and miss noise but much more frequent with a warm car. Also going have #6 scoped just to see if things are ok in there. Seeing as that's been my most consistent CEL.