I gather you have a Glacier lift pump and I assume therefore, that it must be mounted on the frame rail in front of the tank. If my previous suggestion checks out and you have solid voltage to your new pump, I'd start troubleshooting your flow. Run a piece of fuel line from a fuel can to your pump input and try to reproduce your symptoms. Look very closely along all lines for any signs of fuel leakage and thus air entry. Do the cheep and easy things first and get back to us.
Quote: "Does the glacier lift pump setup run through the same wiring or does it require its own wiring?"
You really should run your pump through a small 12VDC ISO relay, with #16awg rather than directly off the stock pigtail. However, it should still work without.
Kevin