water pump???

HELP!!! I have a 1999 New Beetle, it overheated the other day, I did the jumper thing with the plug on the bottom of the radiator, only the small fan worked,,,I removed the big fan, It tested inop,,,I replaced the big fan with a new one and the thermostat at the same time, Now the fans test fine but I dont think water is flowing,,,still gets hot,,top radiator hose is hot, bottom is cool,, no heat inside the car,,,I JUST DONT WANT TO REPLACE THE WATER PUMP,,,any Ideas other than that????? thanks!!
Edit>>>could there be an air lock??

thanks for all the help! this forum sucks!!!