Hi!
What surprised me, though, is the final score.
My score was 9960 (quite low? sorry - no metaverse, havent done one so far, but no cheats, no Ctrl+N).
However, the Arceans were ahead in every single category - tech, military etc. And their total score was less than mine!! How does that work?
Simply: you won, and got additional points for that.
It seems that Industrial Sectors sucks
Very true.

After a bad experience with ISs in one of my games, I avoid building them on regular tiles (only using them on bonus tiles).
(AIs got) In one case 700% research and 300% research and in another case 700% mfg!!! Is this how the AIs are boosted at the higher levels? Or is this just random?
AFAIK random. They just got luckier with the planet draw. On higher than "tough" levels they got bonuses to almost everything, up to 400% at suicidal.
how does one ramp up ship manufacturing so that large ships can be turned out at least every 2 turns?
Next to impossible without lots of bonuses on a ship-producing planet, and very strong economy to sustain such a money sink. For a manufacturing capital you need a decent planet (class 10+, OFC bigger is better) with some heavy bonus tiles (one 300% is usually not enough). A moon and a production-boosting event at colonization also help you decide if planet is worth specializing in production. On this (these) planet(s) you build mostly factories and power plants,
maybe 1 or 2 the most needed "wonders" and a farm, nothing else. Then you boost that planet's production with as much econ starbases with production-enhancing modules as you can fit in a given space (up to 24 in best cases!), and you have a planet with several thousands points of production.
However you need to know that for each manufacturing planet you need several money-making planets - the higher the production, the more planets you need to feed that humongous money sink (up to 10-to-1 ratio). Quite often I don't go in such an extreme, and use several less specialized planets, that produce in peace time constructors, troop transports (who ferry population to less populated planets, of just held the excess pop in space), and fake defenders, but can still produce in 5-10 turns a 1000BC worth medium or large hull (I like slow-tech and small games, so my games are usually over before ultimate weapons are researched, and ships costs go into tens of thousands BCs).
BR, Iztok