Years ago I made a scenario like this for SH4 to train hydrophone tracking.
http://www.subsim.com/radioroom/show...&postcount=221
I made heavy use of the waypoint system where units choose to fork off from a string of waypoints with a different speed at a random chance. All of those waypoints (grouped together) forks off to a single waypoint far away that has a huge uncertainty region to randomize the endpoint location. So I made a string of successive waypoints, allowing forking off at different speeds starting with an initial low chance increasing at each next waypoint. So to have an equal likely hood of each speed being chosen.
As for randomizing units you should make the waypoints for a group instead of a single unit. And have multiple kinds of merchant classes in that group, but only 1 may actually appear.
I'm quite rusty on how to actually set this up in the mission editor of SH3/4. But it is the gist of it.