5 speed tech

To the best of my knowledge the gear ratios are the same.

IMO, the most likley thing to bite you is the Output Shaft Speed Sensor (OSS). This is used by the PCM to measure the car's speed.

I am reasonablly sure that in 2004, Ford changed the number of teeth on the OSS reluctor wheel.

While I am not a transmission expert, I believe it is possible to swap reluctor wheels. However, some disassembly of the transmission will be required as the wheel is on the output shaft.

1-4 are the same ratios, OD varies between .62, .68, and .72. Reverse is 3.38 except on the TCET2070 and TCET5852 versions (4.38). According to Tremec http://www.ttcautomotive.com/english/media/pdfs_autogen/TR-3650.pdf

My 2002 GT has the .62 OD gear, although I'm not sure exactly which revision it is.