This might seem stupid but did you forget to take the trans-axle shifter out of neutral and put it into either High or Low Range????
Other than that, you need to make sure that the pump is spinning, that the screen in the reservoir tank is not plugged, that all the clamps on the inlet hose are tightened down hard and that the reservoir has adequate oil.
If you are using the same pump, travel control valve and drive motor as you did prior to the engine rebuild and everything worked OK previously, then this can't be a big deal. There is no such thing as priming any part of the system. The reservoir feeds oil via gravity to the pump. If the pump is spinning then it will pump that oil throughout the entire system in a few seconds.
It does not matter if the lift circuit ports are plugged. That has no bearing on your problem.