Can a custom recipe call an item from another mod as an input or output (assuming, or course, that the other mod is run at the same time) or will that just crash the game/not show up/cause other errors?
Yes, it can. The game loads item list before loading recipes for them, and thus it's only required that the item is there at all, no matter in which data file. In fact, this is the same reason for which expansion packs can have recipes which use ingredients from the core game, and the same reason for which mod-added items can be crafted using core game ingredients as well. The only "problem" here is the fact that doing it this way makes installing your mod less idiot-proof, but that's not something you ought to concern yourself with, really.
