I've replaced the throttle body gasket, changed the fuel pressure regulator and the fuel rail to a new stock setup. My father and I replaced the intake and exhaust manifold gasket, checked the vacuum lines and seals with intake cleaner.
The engine still began to have idle fluctuations at about 20 minutes after we started it up again.
There's no missing or sputtering and the idle is smooth until it enters what I assume is closed loop however, when the O2 sensor is unplugged it still has the surging idle after 15-20 minutes. The spark plugs are sooty as the engine seems to be running rich.
It is weird to me that I was driving down the road at highway speeds just fine when it begun, it felt like it was bucking so I coasted into a turn out, let it cool and it ran fine for a couple more minutes down the road till it resumed, I then got it towed back home and been woking on it since.
I am thinking of moving towards spilling the cash on a new PCM/ECM as I am well into firing the parts cannon, as we say.