You are saying the fuel pump was not working, then after you took it off it started working again - it is intermittent?
It only puts out a few PSI, its not like a 40psi pump for a fuel injected engine.
Normally when you turn on the key it runs for a few seconds while it tops off the float bowls and pumps them up to maybe 4 or 5 psi (off the top of my head). Then when the floats open and it needs more fuel, the fuel pump switches on and off as needed.
If you wire it directly to the battery 12V it should run all the time, and I would think if you are getting any flow its probably ok. Maybe there was a bad connection on the fuel pump circuit, or maybe something got sucked into the fuel pump. Make sure your bike has the inline fuel filter after the petcock. Sometimes they get plugged and people take them off, and never replace them.
Carbs should not just suddenly plug up unless you got bad gas - sometimes a big thunderstorm will run water into a gas station's tanks, and you end up with water in your fuel tank.