A new vehicle comes with a better tranny. Sarcasm aside, I am a retired engineer. The engine's and tranny's computer are programmed for that engines torque curve and the gear ratios and number of gears. So, lets say you get a mechanical fit, for the purposes of illustration. Now you have to find the computer with software for a 20 yr old engine, which incidentally was not offered past 2006 (I think) in the expy to run a 6 speed or greater tranny and find a tranny computer that is set up for that engine so the computers can talk to each other.
In engineering jargon this is called reverse engineering.
Note: the usshift unit manufacturers website shown above, give me in impression that their unit is an after market device to improve an existing unit, and the 2003-2004 expy is not specifically listed. However, but what do I Know?