I just put a 98 SVT tranny (cable shift) into my 95 SE (rod shift). YES, it's a mojor PITA!! The newer shifter assembly was never meant to go into the older body style Contours because the rod shifters dropped straight through the floor. The cable shifters run the cables along the interior of the car then through the floor board. I'm not sure where exactly they're supposed to come through though.
In mine, the rear under seat floor vents come down through the center of the dashboard and then split where it meets up with the floor. I had to cut part of the floor board out in order to fit both the shifter assembly and the cables. I'm not sure about all of them, but the only place I could really find to put the cables was RIGHT in front of the shifter. I cut about a 2"x2" hole in the floor and screwed down the cable mounting bracket. It's a REAL tight fit, but it can be done.
And the shift tower DOES NOT need to be changed out in order to do this, but I do highly recommend it.
Oh yeah, and the bracket on the tranny for mounting the cables to the housing is a tight fit to the brake lines. I had to slightly bend the brake lines (be extremely cautious not to kink them if/when you do) in order to keep from making contact between them and the counter balance on the one shift bar. I also highly recommend connecting the cables before fitting the transmission back into place to the engine.
Just my 2 cents worth!!