Lol I'm pretty sure that's actually how she got her borken legs, a crowd of giant thrips zombies swarmed her and knocked her over, but thatnks to her armor they never landed a killing blow, instead just breaking all her leg benders and ripping the cartilage in her ears (which is annoying, since it doesn't heal so her tile is always flashing as if wounded but she's perfectly fine now, pretty much).
Anyways, caught another bug. For the rainbow extrapolator blueprints, the reaction is trying to make an ITEM_TOOL_BLUEPRINT_COLOR_EXTRAPOLATOR, but there's no such item - the actual blueprints have the item name of ITEM_TOOL_BLUEPRINT_RAINBOW_WORKSHOP. This is freaking out the reaction and making it produce random tools, none of which are actually usable as such, and so a rainbow extrapolator cannot be built. Just change the item name in the reaction product and it'll be fixed.
Also straw beds are not taking their material properly. They can be used as beds, but are just named "bed" with no mention of straw anywhere. Not sure if this is intentional. Cloud beds and other furniture seem to be working fine, if having the aforementioned problem of not being stored anywhere. (The same for the cloud seeds/light clouds/heavy clouds, which results in a cluttered weather factory really quickly).
Every other industry I've gotten running so far seems to be doing just fine, though - I've got a ton of apples, clouds are fine aside from not being stockpiled, study is producing tomes automatically, etc.
Edit: Just built a crystal forge...are high-value gems supposed to be body parts? It's calling for an "unrotten GEM_HIGH_VALUE bodypart", which, looking in the raws, you've added USE_BODY_COMPONENT and UNROTTEN to the gem reagent. I'm fairly sure this will block normal gems, as USE_BODY_PART insists that it's a CORPSE or CORPSEPIECE, so we might not be able to make crystal shards from high-value gems unless there's a body with the needed reaction class sitting around. Removing those two tags would fix it, and if there's some animals you're planning to make into crystals, a separate "Process Crystalline Corpse" or something reaction would be best.