To cgtech's point, anything that may have been submerged, I would disassemble and inspect closely. There was a thread not too long ago from someone rebuilding a flooded cart. They showed a picture of the motor and it was full of all kinds of junk. It ran before they took it apart. Here is the thread:
http://www.buggiesgonewild.com/elect...ighlight=flood Post #15 they posted pictures of the inside of the motor.
As for which controller to get. That really depends on what you will be using the cart for, and/or what capabilities you want to have...