Yeah, this machine has 3 gigs of RAM, so it's not hitting a physical memory limit there.
1) About 41,000 ships between us and the AI.
2) We're 16 hours in, it probably started around the 12 mark. We play on epic, with normal ship caps, for what that's worth. This isn't an atypical game size or length for us, and we've rarely had this problem in the past.
3) Not at all, actually, so I don't think that's it.
I've attached a save, if that's any help.