Lines break, even 4 ft down. It just makes it harder.
Pictures would be a great help, but here are your options:
You've got a air bubble in the twin line setup that is hard to get out. What happens when you put water in the smaller pipe (drive pipe)? You should get water all the way back through the suction pipe, which will be the larger one. If they are both the same size just try to flush water through both of them.
You could have trash in your jet, but it should still pump, just no pressure.
Doubtful your pump is bad, but I suppose it's possible. What is the model #?
The footvalve could be stuck shut or open. I'm unsure what you mean by "won't prime". Sometimes they will prime but won't pick up or pump, and sometimes they just simply will not prime and stay full of water.
Also there could be an in-line check valve somewhere in the buried line.
When you say you can't get water out of the two holes do you mean when the tank side is pressured up no water comes out of the back of the pump where the two lines are? The pump might have a regulator on it and sometimes they won't let water back into the pump. Try pouring water directly into where the gauge is until full.