I'll make an attempt here...
This from the LMR website:
"If you have a U as the first digit, the vehicle was manufactured with a four speed automatic, 4R70W Mustang Transmission
Some of you may be wondering about the other 2-5 digits. They are related to your Mustang's springs, front/rear which in this case, does not help you in identifying your Mustang transmission."
However, if you have a five speed manual (? which is unclear from your post), perhaps the car was recipient of an auto to manual transmission swap sometime in the past. In any case, I recommend you use specific transmission visual clues for identification. If you post pictures here, I'm certain someone can help you. Happy hunting.