It sounds like there is a partial restriction inside the tank outlet (debris collected down in the outlet bowl on the bottom of the tank). Your new transfer pump can pull harder - so it is delivering some fuel. But it could also be pulling in some air somewhere - maybe around the selector valve on the filter housing. Any air in the injector lines will cushion the fuel pressure pulses and the injectors won't spray fuel like they should.
First, try carefully blowing some compressed air back into the tank through the fuel tube that leads to the filter. That will temporarily push away any collected skudge and the tractor should run better - may need to bleed the injector pipes again. If this helps, the tank needs cleaning out. It takes some doing - sometimes the last few crumbs need a vacuum cleaner. I had to take my tank off and dump it out - there's a baffle partially covering the outlet so its not very accessible thru the filler neck.
BTW, if the tank outlet is unrestricted these tractors will run ok without a transfer pump - just need a full tank.
Hope this is useful. As always, prompt cheerful refund if advice turns out to be bogus. Dick B