1994 Mercury Cougar transmission problem

My 1994 Cougar has 40,000 miles. When I am traveling along the engine will race and the RPM needle shoots upward. It is doing this more often of late, t will do this three or four times and I can visibly feel a sort of clunking sound and it will be okay and it could repeat this three or four times before it's okay again. I have had to pull off the road a few times because when I step on the gas, it doesn't react. There is no particular speed I am doing when this occurs, no uphill/downhill incidents, etc. I go the same way to work every day and I can tell exactly when it will start to act up. There are other times when it doesn't occur at all, but this is become more rare. My mechanic thought that maybe it needed a new transmission and advised me to call Ford Motor Company because transmissions don't become a problem at 40,000 miles. I called Ford and they checked to see if other Cougars had the same problem and there haven't been any complaints. Is there something else it could be besides the transmission? It just had a fuel injection cleaning, tune up. Please help!