We've been using this mod for at least a couple of years on 2 clusters. Suffice to say, removing it is more than a little inconvenient. In order to soften the blow to everyone on our cluster, Here are my thoughts:

(I doubt this will work but would be cleaner if it does)

Step 1 - Spin up a new server without the stack mod and set stacks in INI to match SMM.

Step 2 - Have everyone transfer all their items to the new server. Theoretically, stacks will become vanilla. However, in my experience, they'll simply poof out of existence. It may be worth testing though.

(sloppy, time-consuming, painful, but will work. Mostly.)

Step 1 - Give everyone a week to craft out as much of their materials into grindable items like saddles, armor, weapons, etc.

Step 2 - Remove the mod. Use INI settings to set stacks. Set the grinder to 100% return and set harvesting, crops, and such to 4x our normal rate for, say, 2 or 3 days to recover things that are hard to grind back out like ammo materials, berries, veggies, etc.

Option 2 is likely the only way to make removing the mod not suck COMPLETELY, and does open up the floor to min-max players to cheese the system to wind up with more than they went in with. But I'm willing to accept that to get my regulars to not be left with nothing.

I'm open to other suggestions, as I'm no expert in these things.