Nice update!
Typos (you asked for them on reddit last time, I don't see a post from you this update though so I'm posting it here):
Mechanics student > Bet I can get it flying: Univeristy -> University
Examine the clockwork isle: speheres -> spheres
Specular armillary description: mechanims -> mechanisms
Watch the production of alkahest (log entry): uinversal -> universal
> Ask about Alkahest: distainfully -> disdainfully; enourmous -> enormous
> Observe filtration: flamable -> flammable
Examine the malachite hive > Look for a place to start: reparing -> repairing
Invite Gelee > The flowers: yeild -> yield
Victory message for maxing all the resources: gagues -> gauges
Is "cthonic" (hadean chronometer desc) correct? It's not a real word, but it's hard to tell.