From my extensive testing after all the fixes and changes I've made, Input items with custom names seem to now be working fully with shapeless and shaped recipes in 1.8 through 1.14.

It also seems to be working with furnaces now, though I'm not 100% sure it will work all the time. Furnaces are a pain to work with and there are still little issues.
Most importantly though, there doesn't seem to be any kind of issues causing duplication. Just sometimes an item will be spit out when it would've been a valid input.

The recipe discovery shouldn't be spammy now, it will just show one notification for a few seconds.

Please feel free to PM me about any issues you run into. Thank you