While I purchased your scenario when it first came out, I have yet to actually try it.
That being said, I noticed in your post that you have used zillions of reference points for some purpose. I haven't looked into why you did that, but I wanted to pass along my observations from when I did the same thing.
I was so proud of myself for creating an area like yours for a scenario that I was working on with all of those reference points that I marveled over it for a full day before I tried to play the scenario. When I did, I discovered that the scenario slowed down so much that I couldn't figure out what the problem was. Eventually, I began eliminating the reference points and the scenario began to speed up. Ultimately, I eliminated most of them and the scenario was back to working the way that it was supposed to work.
I'm not saying that you have anything wrong with your scenario. (Again, I haven't played it.) But, if you suddenly notice a tremendous slow-down, you can bet on it being associated with the inclusion of too many reference points.
Just food for thought.