I am pleased to report that dispite my lack of time working on civ and the Star Trek mod, I have finally got a huge chunk of the XL map done, and I have done some debuging/unit combat testing. I think I'm very close to fixing the unfair combat problem. The exact results are:
at April, 2119 AD, the Vulcans and Andorians delcared war. P'jem was conquered by the andorians, but after a few turns, the Vulcan AI (mysteriously) filled a transport w/ four Minor Infantry and sent it to Andoria, where they fought and conquered the system!
Meanwhile, the Rigelians and the Suliban declared war. The Suliban lost 2 systems to the Rigelians.
Conclusion: the AI seems to be liking the new unit stats. I still want to balance the defence bonuses out a little, to make easy conquering less likely, and I want to check other eras, but so far it's looking good.