1. No.
If it's REALLY important then don't use waypoints: replace each waypoint with a gamelogic surrounded by a trigger. When the group enters the trigger area, it gets a move order to send it to the next gamelogic. Thus the order to move to the next GL is given just before reaching the first GL, so the group doesn't stop.
However, it might be easier just to go through your waypoints and remove most of them. The pathfinding in this mission is good, you only need to put a waypoint in a place if you really want the group to go there.
2. Some older unpbo utilities do not decrypt the official missions. (You had to run a seperate dos programme for that when I was a lad. Getting electricity to the computer was tricky because we lived in a wet paper bag in the middle of the road.) Use Amalfi's unpbo 1.5 from the Editors Depot.
And you are absolutely right, examining BIS maps is one of the best ways to learn.