Okay:
1) Glass
There's no obvious reason to need to grind stone into sand before making glass, since you're just melting it anyway. It might take a bit more fuel (which you could add in the custom reaction as an extra fuel), but you could use pebbles or chunks of silicate stone instead (which can be abstracted as just boulders)
Also, sandstone isn't particularly pure to be using, but might work still for low grade glass. Quartzite would be much better as a mineral alternative to sand. If you want to be super thorough, go through the basic stones and figure out which ones are silicates. There are probably a dozen+ of them (quartzite definitely being the most pure).
If you want to be realistic in glassmaking, you would want:
* Silica (sand, quartize, possibly sandstone though rather impure, etc.) ~4 parts
* Flux stone ~ 1 part
* soda ash (burn certain plants, then similar process to lye making with their ashes) ~1 part
However, I'm not sure exactly if you care, or how you would override default glassmaker reactions or if it would be worth it. I believe you can mod what object you get from the sand collection job, which you could change to something other than sand (a clone of sand that you control the reactions of) in order to override defaults. *shrug*
Sounds more like my kind of mod than this, and would make things more difficult (which also then demands more usefulness and opens a whole can of worms) Just thinking out loud. At the level you're messing with glass, maybe just allow various silicate boulders to take the place of sand and leave it at that.
2) Nethercap
I really like youridea of grinding up nethercap and using it to make crazy cold materials of various sorts, that's amusing.
It doesn't really make sense for any sort of ceramic though (or anything else heated, like iron), since the nethercap would prevent you from firing the clay or melting the metal, etc....
Possibly some sort of nether adobe air dried substance? Dunno. This is obviously all fantasy stuff, so whatever strikes you as reasonable, as long as it makes sense as being ice cold all along the manufacturing process. But ceramics and metals don't seem like good candidates.
Maybe some sort of nether concrete? That's a cold process that yields a useful product type.
* 4 parts Gravel (add some way to make it. Could be as simple as a crushing block workshop that just takes a stone block and a pick to build. Or as complex as a clone of the quern that requires certain very hard materials to build? Or maybe just any building material + one diamond, ruby, sapphire, emerald, or topaz? Sounds expensive. I dunno. Your tungsten would work too if you add it.)
* 1 part nethercap dust
* 1 part flux stone (representing slaked lime)
* 1 part ash
= several ice cold concrete boulders usable at the mason workshop, mechanic's, etc.
3) Anthracite would probably yield more coke per job, but is still too impure for lots of the things DF uses fuel for in its raw form. You should still have to refine it.
4) Most of the weapons changes are pretty fantastical here. Tungsten and brass swords etc., but you seem like you want a lot of crazy metals as the core concept, so okay!
5) Races are already modded up the wazoo - make sure there aren't already versions of exactly what you want before you sink a ton of effort into them.