Sorry to butt in as a non-plumber, but did you ever solve this?
I'm wondering if you don't have air in the line from well to pump - if you ran dry at any point in the past then you have to get ALL the air out of the line before it will work properly.
I don't have a well per se, but a culvert off a creek near my house. Foot valve in the culvert, line to the house, jet pump (and pressure tank) in my crawlspace.
Usually annually (sometimes more often, sometimes less depending on how closely I am paying attention) the intake between creek and culvert silts in and the culvert runs dry (and thus zero water at the house, and air sucked into the line). When I prime the pump again after incidents like these (once I have dug out the silt, etc. and there is definitely water in the culvert) it can take HOURS to get all the air out of the system so the pump can get enough pressure to get up to 40 psi and finally kick off.
My technique is turn off the pump (convenient switch in the crawlspace), pour as much water down the line (through the pump prime hole, yes I need a better system but have never gotten around to it) as will stay without overflowing, close the priming plug, turn the pump on, wait until it hits whatever pressure it can hold and doesn't climb any more (often nothing for a while), shut the pump off, undo the priming plug (very slowly), let all the air out (in later stages it will be under some amount of pressure and followed quickly by water, so do it slowly until water rather than air starts seeping out, then shut it again), and do it all again. And again, and again, and again....sigh...I also have a tap turned on upstairs in the house to help with the process, but shut off the supply between the upstairs and the pump when I shut off the pump as in later stages the water left in the house lines can help the priming process.
You will get running water with air still in the system but you'll never get the pressure you need to get the pump to reach 40 psi (or whatever it's set at) and shut off. And you would also have that symptom of water flowing back into the line (almost as though you had a faulty foot valve) until all the air is out. I've found that once I can get to 25 or 30 psi usually the rest of the air will clear out through the open tap in the house, but not before that. So maybe see if that is the problem?
As I said, I'm NOT a plumber but am (unfortunately) intimately acquainted with my water system out of necessity, and as I read this thread I thought hmm...that sounds familiar (I actually have instructions for myself written a few years back complete with the time it takes to prime the system posted in my crawlspace so if I go a couple of years without having to do this I know when to give up and go drain the culvert and take off the #$$^()& foot valve and clear out tree roots or mud or what have you). Which is another thing to consider, but I'd look at the air issue first.
Cheers,
Lelani
One other note for anyone with systems like this that have the potential to run dry - if you ever have a situation where the water isn't coming in (pump running constantly) and there's any chance the foot valve has failed, TURN OFF your hot water tank right away. I've had my foot valve go and siphon all the water out of the hot water tank and burn out the elements as a result.