so I broke a tooth on the supercharger where it connects with the water pumps can it be replaced or can still operate the same with one tooth

 

Moved to the Stock Problems/Issues area.

You pry the pump out without first removing the flange bolts at the motor block where the water enters?

 

Yikes!

I can't imagine what one would have to do in order for one of the water pump drive tabs to actually break off...

 

I've seen this before and it's usually from pulling the pump off with the supercharger still bolted to the block due to the tilt you put on the pump. So I would try to find a new rear section to rebuild the supercharger with and make it right.
Also make sure you clean the block up before installing the flange as that looks really bad.

 

Was waiting for a seasoned pro to chime in and Way Motors fits that bill to a tee.