Hey!
I was hoping to get around to tidying up some of those loose ends with cruiser command, but with college work, and with starcraft 2 on the horizon; it probably won't happen.
The main thing that needs fixing is the vessel selection bug. This is caused by the looping AI triggers bumping the map over the stack overflow limit. The best way to fix this would be to remove the huge 'pick every unit' actions. The game needs to process each unit 1 at a time. This was partly why I started natural selection; to test how an optimised AI would work.
I must warn you though, the triggering is incredibly sloppy and untidy; I can point you to specific triggers if you want to change something in particular, but I haven't exactly made the process easy :S
Still, if you want to give it a try, I'd be happy to send you the unprotected
What's your e-mail again?