All her room stuff being available is a bug (I left in a condiitonal override from debugging). I'm sad/sorry about that since you're supposed to progress those scenes in parallel with her submission route, wherein they'll make a lot more sense.
Koda- I somehow have 3 invisible threads in my inventory (completed all content) without crafting any of them, how did they get there? I know there's probably a way to get them but I haven't figured it out.
Invisible Silk is currently a Lucky Bonus (10%, but upgrades to 30% after conditions are met) from S-Ranking Jessica. I won't spoil where the the freebies came from but they were a one time gift so don't worry about having missed a step. You've unlocked the increased drop rate as well.
I'll probably increase the rates further to reduce the grind since initial feedback seems to be that S-ranking Jessica is a fun challenge (for normal saves) but the loot RNG pushes it to tedium at current #s.