Changed the rearend gears now line lock and rev match does not work? Any help would be greatly appreciated.

 

What year/make of car.

 

Posted in the S550 section so that is my guess for year/make/model. And I don't think any prior Mustangs had onboard line lock.

Did you adjust the tune for the new gears Stangman94? If not, then the computer isn't getting input it is looking for maybe.

 

JimC is probably right with that diagnosis. These modern cars are really tough to modify with all the computers and sensors.