95 Contour 2.5L V6 Transmission Problem

95 Ford Contour with a 2.5L V6, automatic transmission, and about 118,000 miles. Just replaced water pump (don't think there is a connection), now, while driving down the road, the engine will race up 1000 to 1500 rpm. It feels like the transmission becomes disconnected from then reconnected to the engine. This will happen sveral times in rapid succession usually accompanied with a fairly violent 'clunk'. Makes me think that the engine and transmission are being dissconnected with a relay or something. I haven't adjusted or messed with the transmission linkage. This usually only goes on for 5 - 10 miles or so and then subsides. Using the O/D Off button seems to affect, but not eliminate the problem. I checked the transmission fluid, looks OK, doesn't smell bad, and level seems to be OK. Please help.

The Check Engine works but does not come on while this is occurring.

Since I had just replaced the water pump before this all started, I thought that I may have caused a problem with the gear position connector (located in the way of removing the water pump). I moved hoses and checked, didn't find any obvious problems other than insulation brittle and cracking off. Re-insulated, plugged connector back in, connected hoses (at thermostat) and tested. Did not fix problem.

Something else that occurred but I don't see any connection is that my crankcase was filled with water! No kidding, listen to this. The water pump failed and the car overheated just as my wife arrived at her girlfriend's house. The girl's father offered to help and figured that since it overheated, it must need water. Not seeing a radiator cap, he removed the engine oil fill cap and poured nearly 5 gallons of water into the engine before his buddy pointed out that it was the engine he was filling and not the radiator. They immediately drained the engine (the car had not been started) and refilled with the right amount of oil. They then sent my wife on her way. Later that day when I heard what had happened, I changed the oil and filter again. Like I said, I can't see how this would cause a problem with the transmission, but just in case, I wanted to relay as much info as possible regarding the events leading up to the problems with the transmission.

Any suggestions? I have searched several 'ask the expert' type sites and left the story, but no help yet. I can't afford to take it to a shop so I'm on my own. I guess I need to read up on how this transmission works and is controlled. If anyone can recommend a good resource for this I would appreciate it.

Thanks for reading.