Alright I'm feeling like I'm starting to get some mixed advice. I thought these tractors have an in tank pump as well as a mechanical pump
Keep this in mind: I know jack squat about your model.
It it does have both, like you said, there is a electric "lift/supply pump" in addition to a mechanical injection pump...
Hang with me...
Before you changed the filter, and introduced air into the system, the injection pump was both pushing and sucking fuel. The electric pump is not supplying enough fuel. (This was a common problem on the early 24 valve Dodge Cummins trucks. The in-tank pump would die but the truck would still run and as a result the injection pump would fail)
Check the electric pump to make sure it is pumping strong.