1995 4Runner 3VZ-E engine Code 12 but good and clear NE;G1; G2 signals at ECM

The issue started with engine die at traffic light but would re-start
Had CEL 12 14 throttle position sensor and knock sensor.
Did start and run reasonable at a fast idle but had no power and seemed to be on Fail Safe Mode.
Changed Ignitor and tested Ohms on NE, G1 and G2 distributor coil. everything OK.
Changed plugs and wires.
Only code 12 came back and stays there without turning the CEL ON. CEL remains OFF but code 12 present and runs better when cold and just started but does not idle at 750 RMP. Idle is mostly 1,100 RPMs.
Run Hantek Scope on NE, G1 and G2 rigged on the bench and moved with small drill3/8" Signals are good and clear, pictures attached.
Check the NE, G1 & G2 with Hantek Scope at the ECM back probing with engine on at fast idle and go the same good signals that at the Distributor when rigged on the bench at close to idle speeds.
Checked the throttle position sensor with Scope and seems to move the signal without and glitches and smooth, so I assume no problem with the TP sensor.
Checked Ignition coil Ohms and within FSM values
The engine seems to idle too high even after warming up and when loaded while drive testing no real power, with some cylinder/s missing.
Secondary ignition waveforms seem OK.
Checked fuel pressure and pressure regulator and within specs.

How could it be that NE signal and G1 & G2 are present at the ECM, however the Code 12 is still there and the engine runs horrible?