So I bought the truck (manual 5 speed, ~100k miles, small cab) a little under a year ago and had a CEL for the engine running under temp. I replaced the thermostat, which had 3 holes drilled in it. No more low temperatures, but once the engine warms up it is at the upper range of hot on the gauge and the OBDII sensor says the coolant temperature (which is the cylinder head temperature?) is at about 224 where it tends to stabilize. Highway or idle, about 220-224 or straight up on the temperature gauge. Higher revs do bring down the engine temp gauge, but otherwise it just runs hot. So far, I've replaced most of the cooling system (heater core was leaking and bypassed, fan clutch was weak to where I could stop with my finger, replaced the water pump since it seemed like not enough coolant was moving, replaced the radiator because it had some buildup), but it's still running hot.

Otherwise I have tested for:
Oil level - normal
Exhaust in the coolant - Test was negative,
Compression -it was high at ~225 PSI on each cylinder but consistent between them
Vacuum - Vacuum does not stay low when revving the engine according to the scanner (I was wary of maybe an exhaust obstruction)
Cylinder borescope - cylinders do not seem to have much carbon buildup
OBDII values - Nothing seems too obviously out of range
IR thermostat - When looking at the black hose going from the engine to the heater core I'm seeing it at about 200F, which does seem hot and not unrealistic when seeing 224 for the CHT

I'm not sure what to look at next. Do I just replace the thermostat with the one with holes drilled in it and keep an eye out for the next symptom? I don't want to overheat and blow a head gasket.

 

So the O2 sensor readings seem like they might be suspicious? With the engine warmed up I see:

O2 Sensor1 Voltage: 0.625V
O2 Sensor2 Voltage: 0.815V
O2 Sensor5 Voltage: 1.275V
O2 Sensor6 Voltage: 0V

My understanding is that there should only be an upstream and downstream, so sensors 5 and 6 seem like they are not actually sensing? I'm guessing that Sensor1 is the downstream. Should that be closer to 0.45V?