$3100 to rebuild a gas 46RE??? Id be shopping around if I were you. Should be able to get that done for about half that price. The most expensive one I ever have done was around $1800. That was with some major carnage inside. If all of your hard parts and pump are ok then it should be a lot less.

Common problems are bad torque converter lockup clutch. This usually leads to other problems if not addressed quickly. The debris from the TC clutch can do a lot of damage. The scenario usually goes like this... First it will cause the governor pressure solenoid to hang up and the trans will not shift correctly or take off from a stop in the wrong gear. This causes even more debris to contaminate the fluid. Then it will slowly start to plug the transmission cooler and sump filter. The check ball in the cooler line will also start to stick at this point. Once all of these things start happening the cooler flow will be not enough to provide proper fluid temp control and most importantly proper lubrication to the intermediate shaft. with not enough return fluid from the cooler the shaft will seize in the OD piston retainer/intermediate shaft support. At this point its game over. The trans is done. Bottom line is if you start having trans problems find out what is the cause and fix them immediately. Keep driving them and they will self destruct.