While we're on the issue of stone, is the alchemist experiment still supposed to cost 10 stones? That's a huge price now (equivalent to 40 stones worth of raw material in 0.34.07). I understand it was intended to "get rid of unwanted stones" back in the older versions, but now you have to do a bunch of extra mining just to get enough stones for it.
I've been wondering about this too. As someone who builds a lot of above ground structures/ fussy with my interior decor and also turns off migration (I hate being dumped with 20-60 new dwarves every season that drink all my booze like little bearded locusts), I tend to have quite small forts and with the new vanilla changes I just don't have the stone available to keep up block production, furniture production, stone crafts for early trading, and alchemy all at the same time any more.
However, in my musings I also took things a step further than just lowering the boulder cost as my thoughts kept getting drawn to how to make alchemy feel more plausible (even in alchemy it was traditionally lead in to gold (or not as the case may be), not some random rock they found on the ground in to gold) without distancing it from it's surrounding fantasy settings, which oddly brought me to Narhiril's mention of the new "object of deity" for ritual transformation. Basically instead of "praying for a gods favour" the alchemist would instead "perform a preliminary experiment" (or whatever) and from that they'd get a "preliminary theory" (object of deity) that could be stocked up (in bins!) and then used for regular alchemy like we already have instead of boulders. Basically substituting raw resources with time to try and keep things balanced.
Not that I'm suggesting changes to alchemy are a priority or anything, but I thought I may as well throw this out there since it was sort of on topic at the moment.