It's currently possible to specify a nucleosynthesizer item output amount that's greater than 1 but, unless I missed something, the same doesn't apply for the item input. It would be nice to be able to have custom conversions for a lower antimatter price, since right now making a custom conversion for a stack of items will have to cost either zero or at least 64 mB of antimatter per input item. I guess adding decimal numbers to the nucleosynthesizer gas tank and allowing to use them in custom recipes could be an alternative solution, but I guess it would probably require a lot more work.

It should work the same as any of our other recipe types: https://github.com/mekanism/Mekanism/wiki/Recipe-Type-JSON-Syntax#nucleosynthesizing input for items is an itemstack ingredient which natively have support for amounts: https://github.com/mekanism/Mekanism/wiki/Ingredient-JSON-Syntax#ingredient so for example the itemInput for the recipe could be set to:

"itemInput": {
  "ingredient": {
    "item": "minecraft:dirt"
  },
  "amount": 32
}

To require 32 dirt as the item input portion, of course the rest of the recipe syntax is still needed.

Aaand you are absolutely right. This works without issues

<recipetype:mekanism:nucleosynthesizing>.addJSONRecipe("test", {
	"itemInput": {"ingredient":{"item": "minecraft:dirt"}, "amount": 32},
	"gasInput": {"amount": 1, "gas":"mekanism:antimatter"},
	"output": {"item": "minecraft:gravel", "count": 32},
	"duration": 5 
});

Thank you and sorry about that.