I find the balancing very good. I have to admit I still did a little "cheat", as I found the AI performing pretty bad against the borg. I added "taunting" to the assimilation ability. So allied ships close to a borg ship trying to assimilate will focus fire on it. This way the AI is doing much better against the borg, when they bring enough ships (and it saves me some micro managing in battle).
Just thinking about it, the idea came to me when watching "First Contact", the borg where holding the Defiant and Picard ordered to "focus fire". It might be possible to give this ability a dependency to some high tech "Picard, learn how to fight borg" research. Including an "anti-borg" pact, that enables it for other races when they get allied with Federation.
Sorry, I know you are already busy
Edit: Sorry, I just remembered that I made another change which also influenced the balance. As my allied AIs where throwing so many ships against the borg for assimilation, I seldom saw any borg ships. So I had changed the borg assimilation to destroy the ships after some time and give them some resources for it. This of couse made the AI borg much more dangerous, coming with full "borg" fleets instead of many assimilated ships. I understand that this is a balancing feature and that you put a lot of efforts into it. So please ignore my suggestion.