Your transmission is likely OK, and the weak link is not necessarily the transmission itself but the cooling. In this case, replacing the transmission will not solve the problem and you are likely to get a repeat.
Do you have the stock radiator? If so you likely do NOT have the transmission cooling loop in the bottom of the radiator, but only the air/oil stacked plate cooler. It is easy to check, just follow the lines from the transmission. Do they go to the radiator, or just a cooler behind the condenser and back? For a year or so someone at Ford decided this was a good idea before recognizing the error of their ways. Unfortunately, many trucks were shipped with this configuration. It generally only becomes an issue when towing heavy.
The oil/water cooler in the bottom of the radiator always provides cooling at any speed and is very effective at heat transfer. The air/oil cooler is not as efficient and does almost nothing when backing up or pulling a steep hill slowly, when you need it most! It is good for secondary cooling but NOT as a primary!
The result is exactly what you experienced. Fluid heats up FAST and eventually the front input shaft seal expands too much and starts to leak. Once cool it will seal back up and be fine, well the first couple times it happens anyway, eventually it will continue to leak and then it will need the shaft seal replaced.
The solution is pretty simple, replace the radiator with a slightly later version that has the loop in the bottom and add a couple lengths of hose. If you want you can also add the 6.0 air/oil cooler for additional cooling. No air/oil cooler can compete with the effectiveness of the radiator loop especially at low speed, which you unfortunately are missing. But this is cheaper than a new transmission.
I had this EXACT issue with my 04 explorer because Ford did the same thing, no radiator loop. I did a ton of research on it before discovering what was going on. I then read that it was also an issue on 2000 7.3 autos, because they removed the radiator loop. Let me know if you want more details. You can also try PM member Mark Kovolsky who is a former Ford transmission engineer. He can tell you anything you need to know.
