I had the local Ford dealer install Ford Racing (3.73) gears in my 2003 GT today but according to them they were unable to change the computer to reflect the new gears so the speedometer/odometer would read correctly. I know many of you have changed the gears and I thought it was a simple computer adjustment to get the speedometer to read correctly on the 99's and newer. Please let me know what I need to do and who I can take it to. 

They should have been able too. Of course, we are speaking of a dealer right?
