@GlitterLich
I think I tried fixing it before but it still doesn't work because I have no idea what is causing it (the code looks fine), so I just leave it be after some consideration:
1. The crafting kit disappearing is an issue, but crafting weapon or armor doesn't require anvil, so I hope players ended up using that (since that seems to work fine?). Also,crafting kit can be bought, if the bug happens.
2. The excess blunderbuss and Ancient pistol, yeah, It is weird (I am pretty sure the code is fine too) but you can just throw them away, if you are really worried about it.

I know it is janky, but back then, afaik, all the codes were correct. Not sure why it doesn't work as intended.

I consider it minor annoyance since the workaround (throwing away the guns) is pretty simple.
No.1 still gave me headache though, but I hope that doesn't happen.

Also no, I am still around, but I don't really plan to get into the game's modding at the moment.
Cheers.

Appreciate the comments @KJ, even if the mod author has gone AWOL, your detailed workaround meant I could make the changes myself easily.

Also, the way you currently have it, players can combine Rot Stone with their weapons from anywhere without an anvil. This fixes that problem and fixes the disappearing crafting kits.
However, now, the ancient pistol and blunderbuss remain after combining with Rot Stone.
Solution? Alter the value for both Rot guns to be value=0;
This way, while you keep your original gun if you make a rot gun, you lose the Rot Stone until you smelt it back down. You neither gain nor lose money this way. Plus, Rot Stone is prohibitively expensive and worth more than the guns.
It's not perfect, but I've tested it and it functions.

As for the problem with the sword & dagger crafting kits being consumed on use, it's a problem with your ancient pistol & blunderbuss having the "consumeOnCombine=true;"

For whatever reason, this removes the crafting kits for swords and daggers. I assume it's a problem with base game code because I can't find fault with your logic.

Here's my proposed fix:
Turn back on "requiredForCombining=anvil;" (you have it commented out).
Comment out the consumeOnCombine.

Like this:
requiredForCombining=anvil;
combineWith=pistol_ancient; toMake=rot_pistol; --consumeOnCombine=true;
combineWith=rifle_blunderbuss; toMake=rot_handcannon; --consumeOnCombine=true;

Hey just a note, but it looks like your very first action in the Rotstone_action.txt is missing it's first opening bracket:
Action] ID=swordattack_rot;
applyWeaponBuffs=true;

casterAnimation=swing;
casterAnimationDependsOnWeaponHand=true;

Also, would you mind if I added the ability to craft weapons from my mod into craft stone? Of course, with full credit to you and your mod.

@Gaist Heidegger
Oh, I might have messed up on those. Will take a look when I have the time.
Thanks a lot for trying the mod and reporting the issues!

These are pretty excellent and well-done! Minor things to report:
> Using rot stone with a dagger or sword crafting kit consumed the crafting kits (this was not the case with armor / the other weapon types.)
> The journal entry for Rot Armor has an extra character at the end of the title.

The mod is pretty much done. Enjoy.

Thanks, I am working on more features for this. Nothing too fancy, just finishing up.

Those weapon visuals

Cool mod

Ah, so the time to cover the realm in Ruin has finally come.

[Insert edgy main character Intro Sequence here with aggressive anime theme music]

On a side note, I do hope that you'll pursue adding even more content like this in the future once this one is smoothed out.

Amazing Work