I can try but..since the current masons take all their stones from the stonepile, since it's closer than the spread stones, I doubt it will do much.
Haven't been following this, definitely didn't look at your download, at all but when you define the building jobs it reserves a stone available at that time. Depending on how you choose it, often the closest of the type you choose. If you only had spare stones in the stockpile (or they were the default closest) then they'd be assigned, and thus reserved until dragged off and made into the approprioate structure. I haven't seen many Fortresses
without a surplus of stones, but depending on how much building you've assigned you
might have actually tied up every single loose-lying stone in or out of the stockpile. If not, there's still a possibility that the stones that would still be free to use in the workshops are so far away that they get some kind of low priority, at least by dint of the dwarfs wandering off to collect them keep aborting for food/drink/whatever.
I don't think that's the answer, but it's something to consider.
As for disabling cave-ins, I would suggest you just use a 'cave-in aware' method of digging, instead, and learn what does/does not cause you the problem. Never assign to be dug (or undermined, or isolated) anywhere that could possibly be the sole-supporting tile for another tile of rock. If multi-selecting, don't assume that the 'cave-inable' tile would be dug out already by the time the one that is supporting it is finally removed. Leave the disabling of cave-ins to creating "floating fortresses" megaprojects or specifically if you absolutely
must have an unsupported "checkerboard" pattern of floor/gap. You can avoid cave-ins through knowing how not to make the happen. They're not like raiding parties and hostile wildlife that you can't avoid the chance of wandering into your enclave and actually have to positively protect against them. (Or init/[RAWS] out their possibility.)