Just took a look at the pump after getting new exhaust and cat put on. Moved the intake tube and about a cup of water fell out. Looks like I'm going to be taking it apart again. I've head that there is a valve that gets stuck open and is a major cause of the water build up. Condensation from the exhaust backs up into the pump. Does anyone know which part this would be in the attached diagram so I know what to look for?

 

The typical cause of water buildup in the pump is the inlet tube (shown between the #1 & #2 arrows).