Humm,
When I filled the convertible top pump after I reinstalled the lines, I left the filler plug out of the pump while I cycled the top (place pads underneath and in front of the pump). It may of helped to equalize pressure. I'd also check, if you used teflon tape, that it has not impeded the orifices between fittings. Finally, if you had to rewire, I'd confirm that the switch isn't wired in reverse.
Best of luck!