Now that I've had a week or so to really drive this thing, I've noticed some patterns.

As soon as it shifts into overdrive (45 mph and above) it starts shaking and bucking like the trans can't decide whether to downshift or not. This used to be an intermittent occurrence but now it's every time I get on the highway. It also still has a shaky (but not that bad) idle and the check engine light will come on if it's been idling for a few minutes without fail. I suspected either of the check engine causes (knock sensors or 02) or the EGR valve. The knock sensors are torqued correctly and the wires are plugged in nice and tight but I haven't ruled them out yet.

The EGR valve looked fine and wasn't sticking but I cleaned it with carb cleaner anyway. The ports in the manifold looked good, too.

The 02 sensor connector was all melted, both on the sensor pigtail and the wire harness pigtail. It looked like just the plastic was burned but I ordered a new sensor and harness pigtail just in case.

Checked #1 and #4 spark plugs and they looked too dark. I'm gonna pull the plenum and see if I've become another CPI statistic.

Anyone have any ideas? Something I'm missing?

I'd drives fine around town, starts right up every time and has no power loss on the highway...

 

So the FPR was the first new part to arrive and I installed it today. The intake on the FPR side was cleaner than the nut kit side so it needed to be replaced. Still waiting on the O2 sensor. I took the truck for a drive afterward and was a little disappointed.

I let the truck idle for a while to get warm. The idle was still a little shaky.

As I accelerated up to freeway speed, it lost power and bucked around 45-50 mph in 4th gear just like it always does then the check engine light came on and the power came back and it ran smooth just like it always does.

I think that the O2 is reporting correctly so this must be the knock circuit. How do I test the knock sensors? Is there anything I can do on the ECM end as far as troubleshooting?