Ok, transmission is different from engine mount, they are not the same, so you cannot assume they would replace something that is on the other side of the engine bay. Sure they could have done it, but only with your permission, so if they didn't ask, it might be something they don't do since they are a transmission shop instead of a engine repair facility. As far as the insurance covering it, I hardly doubt that they would cover it, again, it is not part of the transmission failure. The clunking could be the clunking, the best way to find out if the mount is broken is do the following.
With the hood open, sit in the drivers seat, start the car. With the foot firmly applying the brakes, put the transmission into forward gear. While holding the brakes solid and ebrake on, put on the gas a little bit and look to see if the engine lifts up about 3 inches or so. If the engine does not move hardly at all, then try the same in reverse. If no movement, then the mounts are ok. If there is alot of movement and the engine lifts up, then yes, you have a broken mount. That would also be the issue with the heavy vibration too. The mount is solid rubber surrounded by steel. The mount absorbs the shock through the rubber and if the mount is broken, and the rubber is completely or nearly gone, then the steel part is resting on the steel frame and thereofre you have metal to metal contact and a heavy vibration issue with also the clunking issue too. It is not the fault of the transmission shop, you just need to repair the mount and realize the car is 23 years old as that is a wearable item.
Now, if the transmission shifted wierd or dropped out of gear, then take it back to them and have them diagnose the issue. Transmission shops do transmission work, engine repair goes to full service facilities. Hope this helps?
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Friday, February 27th, 2009 AT 11:35 PM