The outward differences are a different reverse light connector and ball shifter cable connector ends (instead of pin). As far as other differences, I understand that the older shift tower is prone to breakage causing a piece to fall into the gears of the trans. That's bad! The updated model, which I think started in the 2000 model year, is supposed to be stronger. When Terry Haines worked up my trans I had him install the '02 Focus tower. In addition to the tower (~$300) I had to get a jumper wire to make my reverse lights work and new shifter cable ends to mate to the new ball ends. Why do it? I think it goes along the same lines as installing a water pump with a metal impeller...peace of mind.
'98 SVT Contour, in at least 639 pieces

4 Speed MTX...synchro and shift fork replacement in progress