I'm just starting the game and I'm loving it, but I can't figure out how to enjoy the crafting and leveling systems which are so clearly crucial to the game.

It seems like all of the resources are completely finite. If you spend too many of those colored rocks upgrading the wrong equipment or gold leveling the wrong heroes, it seems like you'd just be stuck. Am I missing something? Is there some slow grind option later in the game? Some random encounters maybe?

Unfortunately you are right. The amount of resources you can find in the game is finite but the game allows you to spend an infinite amount of resources via two means: crafting and attribute resetting. If you craft too much or if you reset your attributes too much you will find yourself in a situation where you can do nothing that requires resources. This is a serious design oversight in my opinion. If you take into account that leveling and quality of crafting are gated behind blueprints which appear at fixed points of the campaign then the lack of possibilities for infinite resource grinding is really perplexing. At first I was sure the challenges are a form of grinding but no they are one time events. Some design decisions in this game seem really weird.