[Mark Walton]

How I see it working, the AI can be scripted to research the various Ultra-Techs at the earliest point the scripter wants them to start. Then, at any point if they get the ruins tech, they would start researching the resulting ultra-tech.

If they CAN be traded, then I would make the first level of Ultra-Tech just be equivalent to the basic ruins tech. Perhaps, even, remove any items from the ruins tech - you can't build massive planetary shields by getting that tech, all it does is lets you research the ultra-tech tree! This means, quite elaborate ruins items can be added in safety, because ruins tech itself adds nothing to the race. Only if they research the clues they find, can they develop any technology.