Been reading about the Automatic Temperature Control (ATC) on the Lincoln. Turns out it's behaving as designed except that maybe the water shut off is not shutting off under full vacuum. I'm making a record of the answers here in case I need to refresh my memory. Read on if interested.
First there's that mysterious wire feeding continuous power to the compressor clutch. Turns out, it's supposed to power the compressor clutch except when the outside (ambient) temp is cool or cold (maybe below 50-60*F). There's an ambient temp sensor behind the grille that interrupts power to the compressor clutch whenever ambient temp is cool or cold. Otherwise, the compressor runs. (The original system didn't cycle the compressor to avoid freezing the evaporator but rather ran the compressor continuously and throttled the suction line to prevent evaporator freezing) Purpose of running the compressor even when some heat is required is to dehumidify the cabin air.
Then there's the vacuum supplied to the water control valve when the system is off or in AC mode. Also working as designed. Vacuum is supposed to shut off coolant flow to the heater core rather than open the valve as I had assumed. Why the input and output hoses to the heater core were both hot when we were trying to charge the AC system, I'm not sure. That valve was replaced when the engine was installed. I'll have to test it some day.
And, we didn't understand why both suction and liquid lines showed high, nearly equal pressures when, in the end, the compressor was shown to be working well. When we stopped adding refrigerant, high pressure line was over 300 PSI and the compressor belt was beginning to slip. Obviously, the compressor is pumping. Answer might be provided by the diagnostic info. One reason for showing high pressures in both suction and liquid lines is "Engine Overheating". Engine temp got up around 220*. Maybe the under-hood temp is high enough so the liquid line contains vapor and it's blowing thru the expansion valve pressurizing the low side too?
Diagnostic info gives another reason for high pressure on both sides: insufficient insulation on the expansion valve's temperature-sensing bulb. I had it swinging in the air to make sure the expansion valve stayed open.
One mystery remains: there's another power supply wire to the AC clutch which I assumed was the one that was powering the clutch. Not so. That's the one that got the suction line pressure sensing switch in the POA Delete kit to cycle the compressor. This second wire isn't shown in any of the shop manual diagrams so I don't know what it's for. Whatever it's for, it will remain in place, with the pressure sensing switch in series with the clutch. Power from both wires will be interrupted by the suction line pressure sensing switch.