Over reving on start up

Make sure all the connectors are on the throttle body and nothing is binding. Jeeps have a service bullitin about something like this. Try removing the IAC and clean the pintal area or replace the IAC. I have a 93 wrangler and I have had this happen to me. I cleaned it and it worked. Try disconnecting the battery for a few minutes then try it again. This will reset the IAC to MIN. If this allows it to start at a lower RPM then you Isolated the problem. Try tappping on the IAC also. It may be sticking. Either way if anything make a difference then you will prabable need An IAC.Make sure you have no vacuum leaks anywhere. A vacuum leak will hold the idle higher also and the computer will close the IAC as far as possible to compensate.

Heres why you have a high RPM
When you start the car if you have a stuck open IAC or vacuum hose leak the O2 sensor will see this extra air and add fuel to compensate to maintaim a 14.7 to 1 ratio but also the computer will see your foot is off the gas and the throttle position switch is closed. Under this condition the computer will want a precalibrated RPM which is between 660 to about 750 rpm +or- some. It will close the IAC till it reaches this level.

There is no direct connection between the water pump and the throttle. It sounds like in his struggles to replace the water pump, he may have disturbed or damaged the throttle linkage, the throttle body, or MAP sensor.