I have almost everything set to 3X and a few things set to 1.5X. That's all working perfectly.

I want to exclude a few items from the multiplier, for example, the Water Jug. What's the best way to do that? I can't find an option to do that in the documentation or the config file. Maybe I'm going about it the wrong way?

I honestly can't remember if v4.0 had this, but once I've got time to fix v4.1 you'll be able to set IndividualItemStackSize values for individual items and it'll override. Can't remember if that worked that way in 4.0 though