Thanks but I had already done that. What did work to speed up the turn time, however, was a combination of the waypoint systems from posts 4 and 6.
Single ships would travel shorter distances. Then the formed up collector fleets were sent to the MSBA. That cut at least 2/3 off the time required for the "autopilot movement" phase.
In my last game I hit massive out-of-memory problems, though, but I found a workaround.
The problem: upgrading (from the shipyard screen) a whole shiptype with 1600 ships to another shiptype (without useless engines...) would result in something that looked and felt like a memory leak.
The operation worked but afterwards I could not save any more. Never again. As a result, the game reliably crashed upon "winning" when it was trying to create the End Game save. Well damn. No score for me.
The workaround:
manually upgrade enough ships so the bulk upgrade was less than 1000 ships at a time. That way GC retained the ability to save and did not crash at the final moment.
Manually upgrading 500+ ships sounds like a ton of clicking but that's what Autohotkey is for. A keyboard macro did the clickeroo in some 30-60 min while I was reading. Jobs like that are what we have computers for, right? 
So after several days of trying to "complete" this already won game it would finally upload the score... http://metaverse.galciv2.com/index.aspx?g=player&id=17099
But why the saintly alignment? The Harmony Center (or wutsisname) adds another 25% to ship defense and since about 2/3 were military score, every point counts.
I did indeed go with "fewer ships" this time. With Yor + (stolen/traded) terran mining tech I had abilities like +454% Weapons and +506% Defense. Is that crazy or what?
It was a very painful experience, though, (mainly for my wrists...) so not sure if I'll try that again. Are they any more shiny medals than "Top 25"? The medal legend here http://metaverse.galciv2.com/index.aspx?g=legend doesn't show any.
Oh, I don't need first place or anything lofty like that. I won't be playing this seriously enough to try and steal any die-hard player's thunder.
Not interested in the empire dealy, either. You know those T-shirts that say... DO I LOOK LIKE A PEOPLE PERSON?