You will have to look at the scripts for the Fast Travel points, both boats and Silt Riders. These scripts are probably attached to the boat captains and silt strider jockies.
However, a nice 24 hour boat ride is just the thing to get rid of some of the spell effects that we get......
Actually, those aren't handled by scripts, they're handled by the game's travel system (basically just glorified doors).
The travel time is controlled by a GMST: fTravelTimeMult
You'll want to increase/decrease that setting by the same factor that you altered your time scale. Good luck.