I 'thought' it didn't run with the car on, but I suppose it really only says it runs after the car is shutoff when it is very hot, not specifically that it doesn't run when the car is running, so perhaps this is normal.
Have you used a vacuum bleeder?
Are you sure your heater flap is operating?
I suppose you could get a quart of coolant, a turkey baster and some towels and try to fill the heater core..........
I have a long-neck funnel that could work, too...
I had checked the heater flap a few times at different stages during reassembly, but not since then. Since we all know what it means to assume, I should probably check again.
I have used a vacuum bleeder on it before with subpar results. I made sure to follow directions to a T and pull the full vacuum, but I think the heater core bypass mod makes that tricky. I have to cycle the bypass a couple times, and that kills the vacuum. Without cycling though, it seems to leave air pockets.
And yeah, the service manually is empty with regard to when the pump kicks on, as you say. Sir Lotus has a post where he stated it kicks on at 230F, but that is so far outside of the normal operating region that I find it hard to believe the pump was worth having if that is the case.
I also want to force run the pump again. It made a sound like it was stuck when I ran it cold last time, and it only whirred when the thermostat was open. Either the diagram above is wrong then and there is no circulation through the pump with the thermostat closed, or I had a blockage that moved. Really hoping the diagram is wrong...