I have been reading this thread with interest and have not provided any input as I have zero experience with the engine in your car. However, 250 Coupe's recent post got me to the keyboard.

There are some inaccuracies in that post that should be addressed:

First - any internal combustion engine that is air-governed creates manifold vaccuum at idle. Air-governed means that a throttle body containing a butterfly valve is used to restrict the amount of air available to the engine for combustion. This means that at idle, the brake vaccuum booster is under vaccuum - not "manifold pressure".

Second - the sole purpose of the check valve (the in-line filter-looking device) is to prevent loss of vaccuum in the booster under low engine vaccuum situations (low RPM combined with large throttle opening), or should the engine die. It does not regulate the amount of vaccuum available to the booster.

As for the overheating, there are 3 likely causes:
1) Insufficient coolant flow. This can be caused by a water pump impeller that is pitted due to extreme age or bad coolant mix (the pits cause cavitation which reduces the heat absorption ability of the coolant, and also the flow rate). The impeller can also be eroded away. Since you've recently replaced the pump, maybe this isn't the case. But I think you noted that the pump wasn't a good-quality unit, so possibly there's an issue with the wrong impeller? Poor coolant flow can also be caused by a thermostat that is not opening fully (that's the "stroke" referred to in earlier posts. You need to know how large a gap is created between the top and bottom of the thermostat when fully open.) It can also be caused by a lower hose that is collapsing under higher engine rpms. Sometimes, lower hoses have an internal spring in the hose - that can rot away with age.
2) Too much (or incorrect) coolant flow. The coolant must remain in the radiator long enough to allow the heat exchange to occur. Running a motor without a thermostat can cause this. (I know your thermostat is in place.) A previous poster indicated that the thermostat may need to open fully and seat against the back of the thermostat housing, forcing the coolant to flow to the radiator, instead of bypassing back to the motor. If the thermostat isn't opening fully, then this indeed can be the trouble.
3) Insufficient heat exchange in the radiator itself. This can be from insufficient airflow through the radiator. Bent fins, dirt & grime between the fins, etc. A rebuilt radiator that has too much paint can cause this problem. A radiator that has a lot of mineral deposits can still flow good, but the minerals block the transmission of heat from the coolant to the radiator tubes. If the car doesn't overheat sitting still, then the fan (mechanical or electrical) is working fine. If the car doesn't return to "normal" after driving and being allowed to sit at idle - possibly the fans are "weak" - they can keep the car cool while sitting still, but they lack the strength to pull enough air to remove any built-up heat from driving. Once you're driving more than 20 or so MPH, normal airflow should do all the cooling you need.

I would personally think if the motor is running lean enough to cause overheating, it would also be experiencing detonation - pinging. But that's just a guess.