Hey Vazkii, I would like a way to add custom infusions (in-game or external program) for modpack developers. Is there a way to do this or a mod? Thanks!

If you mean infusions in the runic altar, that is already possible. The Regrowth modpack adds a massive number of recipes.
One thing to keep in mind however is that the livingrock at the end is still necessary.
(( http://forum.feed-the-beast.com/threads/1-7-10-regrowth-a-wip-hqm-pack-now-listed.57184/ ))

The thing is, how do they do it? Minetweaker?

From what I can see at the Regrowth repository, they first use Minetweaker (https://github.com/thephoenixlodge/Regrowth-Stuff/blob/master/mods/ModTweaker-2-0.9.0.jar), then use a number of scripts to change the recipes around. Here is one of the lines that seem to add stuff to the runic altar crafting recipes.
Hope this helps, and best of strength with your endeavours!
Edit: Looking a little further, this line apparently adds a recipe for throwing an item into a mana pool.