My friend was the same with his yz85, ran like crap, and the air filter was the problem.
My dad made me read the manual 3x before i rode my bike, but my manual is 80 pages.
And his is 300 detailed pages, now he has to read it, itll be good for him.
There not much else u can do to make it run better, with out making major changes, like a topend, new gaskets, and it looks like ur gonna be busy riding.
Repack the silencer, change the oil, lube the chain, and thats about all you can do, when you dont have any new parts on hand.
Make him buy a couple plugs because youll need them rejetting it, and he can use them after he fouls them out so he wont be losing anything.