100 clicks is roughly 1 square grid in the map. Is this the mission in Muscovy? It's a bit of a pain. I've always failed the first part (distance from portal), but the quest still allows you proceed to the next part, shadowing the transport.

It isn't too much of a problem: you get warning messages when you stray too close or too far. Equip your mothership with the 400 click radar module and keep the transport just within the maximum sensing range. It doesn't take too long, but make sure to alternate saves every few minutes in case you fumble.

I think there was another mission like this but I don't recall where.