The custom milling reactions won't show up for me. Neither does empty water bucket. Come to think of it, I'm not sure if any of them do, other than pearls showing up in the craftdwarf shop. I manually merged raws, but everything looks right (reactions are under permitted for dwarf, tags in place, etc, etc). The new pig iron & steel reactions work perfectly.
Pearls sounded like a great idea, but I was already buried in mussel shells. It's probably more the fault of the mussels being too plentiful, since they can keep a fisher, fishcleaner and bonecarver working full time (this is vanilla, not because of the mod). The problem is vanilla shells are a seperate category and can be regulated to a specific refuse pile. Since you made the pearls remains they go to the remains pile, which already tends to fill up on me (and I have a 75 tile pile for remains). I reverted it back easily enough myself, but I bring this up in case it isn't something that's been observed.
All in all, great mod.