I had been thinking, after some research into various hard tissues for what could be a source of gelatin, that shells would be a good source of flux. The flux stones we have are all forms of calcium carbonate, and shells are primarily calcium carbonate(so they're poor gelatin sources). So why not have a reaction to turn shells into "shell flux" stone?
Rock farming does make sense in universe, and a custom reaction to make it happen should be simple, I think it's already been done, but it's good practice anyway. Though I'd wonder how to balance it. Then again, we can turn fruits and beg into logs, decimating other resource shortages isn't much of an issue. I suppose it could be balanced by making the seed values quite high, so they can't be taken on embark, and with the amount of stones in the game, getting a particular variety of seeds is going to be more luck than judgement, unless you pay over the odds for it.
What new plants were you adding? I think the current biome restrictions on the dye plants might be part of the problem, since my testing tended to show things working a lot better..
Sorry for the slow progress on the update, I've been distracted by Ghost Recon: Shadow Wars(by the guy who made X-Com) and Terraria. After some research with conflicting evidence in every direction, I've decided to make citrus plants brewable immediately into wine. Some sources say that wine made directly from citrus fruits is more like a thin paint stripper than a drink(laraha wine should be especially deadly), and that it should ideally be made with a mix of citrus fruit and either white grapes or bananas to thin it gently and give it more body, and in the cocktail arc I'll make using those produce a more valuable wine. For now, citrus fruits are just used as is, but after the next update I'll switch to having to peel them, so that the peel can be used for liqueurs.