Possibly, the "modifications," i.e. the jet kit, trick needle, and who knows what else, created a seriously fuel-rich mixture. Thus, any intake air restriction (even a clean, properly-oiled, stock air filter) exacerbates the air/fuel ratio's fuel-richness and inhibits higher-rpm running.
As planalp above suggests, restoring the carburetor to stock condition (i.e., stock main jet, stock needle) and running with the stock air filter, might allow higher-rpm operation.
The aftermarket exhaust may want slightly larger jetting, but probably will run fine on stock jets.
I'd consider going back to a stock carb, stock air filter, and modifying from there, if that's your pleasure.
So, don't know the cause or cure for your problem, only--jillions of KLR650s in production for 28 inclusive years ('87-'14), run fine with stock air filters. Unless your carburetor has been jiggered to an overly fuel-rich mixture condition, seems like it oughta run o.k. also, with a stock air filter, IMHO. Doubt an aftermarket air filter or air box modification will solve your problem.