As the title suggests: implement a configuration file to add or remove items that can reduce fatigue when consumed, and an option to penalize or prevent overuse of fatigue-reducing items. (Currently using the 1.12.2 versions)
The first part - additional control over items with fatigue reducing (or increasing) items: The implementation of coffee items reducing fatigue has been a godsend, but there have been a large amount of other caffeinated beverages from other mods (Such as teas, sodas, and energy drinks, seen in: PHC, Simply Tea, Tea: The Story, and XL Food Mod to name a couple) that I noticed and tend to use far more often that should be able to apply the same effect, or even relaxing beverages to increase fatigue, such as the dandelion and chamomile tea from Simply Tea. I can see this implemented as a .json so users can set the item parameters themselves and allow greater control over fatigue-reducing items.
The second part - config option to prevent overuse of fatigue-reducing items: I do want to emphasize the optional part of this, but the idea behind it is the fact that no matter how much coffee you drink, you can't push yourself forever on no sleep. Eventually, it will catch up and you'll crash, or just become too tired to continue without proper sleep.
The first, more complicated idea is a cumulative multiplier to the fatigue rate that ticks up each time an item is used to reduce fatigue, that is reset once the player sleeps properly. Starting low or with no multiplier on the first (So your first cup of coffee or tea that day won't affect it), and creeping up to a high rate over time with configurable scaling and maximums. This way you can prevent players from staying awake forever just by repeatedly drinking espresso, but not removing the ability to push beyond normal limits without sleep for a while.
The second, simpler idea, is simply putting a configurable limit on how many fatigue reducing items can be consumed or how much fatigue can be recovered through items before you can't benefit from it any more, requiring sleep to reset the uses.
Both of these ideas struck me at the same time after seeing the coffee item support added just recently after updating my private modpack, and thought I might offer them up for consideration. And thank you for what may be the best sleep mod for minecraft I have ever used!