Thank you for your patience! I've been dealing with other aspects of my life recently, but I am still working on this.
I am pretty much in the polishing stages now, which involves tweaking cinematics, lore write-ups for the various units and abilities, and debugging as needed. Barring very minor tweaks, missions 1-6 are fully completed. Missions 7-9 should be fairly quick. Mission 7 essentially wraps up the lore write ups, which I am working on now.
Status update: My custom tech trees are finally fully in the testing stages. Work is underway on Mission 8.
Mostly what remains to be done are the rest of Mission 8, Mission 9, debugging, tweaks, and polishes. It's been quite the grind!