I'm having more trouble. The AI won't build any of the new buildings except 1 of the defenses, but only 1. Because of this , I'm starting over with a clean slate(I even reinstalled RA2/YR). Hopefully this will fix the problem. And yes, I did have AI build this=yes and the buildings worked fine, as I built them all the time.
Base defenses in the normal sense (IsBaseDefense=yes and added to the appropriate lists) don't need AIBuildThis=yes.
Planes crash by themselves in the normal game too, this has nothing to do with the cloning bug. It's a PadAircraft bug, it has always existed, and there's no way around it without using BuildLimit=.