Oh, one other note: a big part of the reason for the recently-added "border aggression" mechanic (aside from all of the more obvious benefits to gameplay, the AI's realism, etc) is that it is also intended to prevent these sorts of uber-high ship counts from ever becoming possible. Instead of storing up quite that many ships, the AI would be attacking you with what amounts to continuous cross-planet attacks long before you'd ever hit that point. Either that would wear you down and kill you, or you'd have to neuter planets that were getting too tough, and not be able to get to that sort of late-game scenario.
In other words, really this sort of uber-unit-count game shouldn't exist, the game is supposed to make you die first or kill the AI first. You've just managed to push it further than anyone else, ever, and that comes with some perils. Frankly, I think most player's CPUs would melt before they even hit the point where this sort of thing was a RAM issue. With the other player with 202k ships, he had something like a 3.6 ghz quad core. You must have a beast of a machine, as well!
Anyway, my point is that I really hate saying "there's not much we can do at the moment," but that's kind of where we are with this one -- in most respects we already have addressed that, in the sense that border aggression would probably have prevented your game from ever getting to this state had you started your game in 3.120. That doesn't make your existing game playable, which stinks, but on the bright side if you start it up in 3.120, then disable autosave for a while, the AI would be attacking you with so very many ships that you could probably get your numbers down to 200k or even 150k within a while, if you survive all that (and your CPU does), which would let you save again. That would be my best guess, anyway...
