Transmission Fluid Leaking problems of the 2005 Ford Five Hundred

Driving from sj to la, calif. 200 miles into my journey with wife and 3 kids, pulled off highway for gas. Slowed down and noticed the wrench and check engine lights on and car would only go 10 to 15 miles per hour and revved at more than 3000 rpms. The car clunked hard when put into drive or reverse. Turned off the engine, several times and restarted. Sometimes fixed problem, other times did not. I had car towed to hanford, California, and then again to los angeles-another 198 miles to Ford dealership. I had to rent a car and drive the rest of the way to la and drive back - 198 miles-to hanford-to return the rental car. I tested the car a few times in hanford and when it was at the Ford dealer. From a cold start, the car worked fine. Drove and shifted well with no problems. But once the car warmed up, it went back into limp-mode, clunked hard when you shifted into drive or reverse, and would go only 10-15 mph at 3000 or more rpms. The dealer test drove it and had the same result. The dealer got codes p0701, p0871, and p0961 and said that meant the transmission had internal problems. They said they called Ford engineers who told them the likely problem was when the transmission fluid warms up, it is not properly circulating due to leaks in what they called two variators inside the transmission. They quoted the cost to replace the variators as $3600 for parts and labor of $1200 for a total of $4800 and that is more than the cost to replace the transmission for which they quoted $4500. So they replaced the transmission. After starting, they found a broken transmission mount so they replaced that for another $250 (part only - no labor charge). I test drove the new transmission yesterday. The car no longer goes into limp mode and drives nicely except after it warms up it clunks hard into drive and reverse and wines in reverse gear. Not taking car till fixed properly.