I had a similar setup on 660 densos and step one is to dial in the idle. keep the STFT around 0 and LTFT around 0 best you can by adjusting the global deadtime.
i was running v3 ecm link too, and i now parting out my car
yeah sounds like they are dirty and stuck open. my advise would be to take care of that as soon as possible. same thing happened on my sti and i blew out the piston rings under boost.
hydro test all 16 valves and check for leaks. Check valve stem seals if engine was burning oil. Get gen3 lifters. Clean out carbon deposits around valves and on top of cylinders. Do a port and polish of the head next