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You just remove the fuel line at what ever point in the system you are troubleshooting and install a clear plastic line.
If you are checking the tank/pre-pump connections you can either disconnect the pressure side of the pump and run it into a bucket, or you can remove the small section of rubber hose (approx. 10") between the pump inlet and hard line to the tank, replace with clear tubing, then crank it up and watch the flow. If you go that route, do not leave the clear stuff on for normal operation...it's not diesel rated and may fail.
i think mine is losing prime overnight if i manage to get it started it misfires and shakes for like a half hour even after its up to operating temp
A quick and dirty way of seeing if you've lost prime is to loosen the NPT fitting at the far end of the cylinder head from the steel line that feeds fuel to the head. You can see a lot of air and foam bleeding out if you loosen but not remove the plug. Once all the air is gone, (not likely if you haven't eliminated the quick connects.) straight diesel fuel will bleed out past the threads.
Most likely you will experience what I did at first: an alternating stream of diesel foam, a squirt of fuel, and then right back to the foam again. Back and forth like that.