I apologize if this has been mentioned already, but "Bonus physical level", "bonus experience" and other fatigue "bonuses" need to be renamed to something that better describes what is actually going on. It's a little silly having to explain for the umpteenth time to someone what "Bonus experience" really means.
I do get the impression that in order to make the fatigue work properly, there seems to be additional things that are added to the character--hence the "gained" messages. So maybe rename the "bonus" items tagged on. Instead of
"You have gained a bonus physical level!"
"You have gained bonus experience!"
maybe instead have
"You have gained a fatigued physical level!"
"You have gained fatigued experience!"
It doesn't sound particularly negative either, like "You have lost experience!" would sound.