Update on my mess - pulled all the plugs today, and found another dead plug, had a pretty good size crack in the stem. Also there was one with a small crack in the tip, but it ohmed out good (0.3-0.4 ohms), I still replaced it for a good measure. Also decided to inspect the harness connectors a bit better, #7 was heavily corroded so it got cutoff and replaced (again I transferred the spring clip to the new connector, no finger tips were drilled into this time, lol). Other connectors looked good for the most part, but I gave them some heat-shrink anyways.
Then proceeded to disconnect the controller, figured all I gotta do is kill power to it permanently, so I disconnected its red wire - got in the cab, flipped the switch to run, and what do you know, WTS light came on!!! ***, controller is powered down, why is the light on (in my truck light on means GPR is engaged). Kill ignition, go back under hood, and disconnect the white wire between the GPR and the controller - that's gotta stop the thing for sure! Go in cab, ignition on, and I was correct WTS light stayed off till I used the manual switch - 10 second glow cause it's 30F outside and the engine ran for like 5 minutes several hours ago, she fired right up!
So, in case anyone wants to bypass their factory solid-state controller, make sure you disconnect the white wire, red one won't matter much at this point, but the white one MUST be disconnected else the stupid thing may ground the GPR on you full time and there go your plugs.