Bogging usually means lean. The fact that the engine won't rev-out is probably a good thing...lean makes power, but is also risky since lean mixtures also increase combustion chamber temps. If the stock carb is still in place and unchanged, I would expect lean running. Just eliminating the stock airbox, alone, can require upsizing the main jet, by one number. Adding a race-type exhaust also changes the effective fuel curve, in unpredictable ways. Bottom line, these induction & exhaust changes usually require much richer carb tuning than stock.
First thing to try is lowering the jet needle clip to the lowest groove. That'll richen the mixture as much as possible, with the existing carb configuration. If you see some improvement, you'll know for sure that you're on the right track. Even if the motor runs a lot better, I'd still test it with the next larger size main jet. Ideally, you want to find the rich limit, i.e. the combination of smallest jet size & leanest jet needle height setting that causes rich misfire (the engine won't rev-out cleanly), then lean-out the jet needle height and/or drop-back one jet size, from there to get optimal performance across the revband & throttle opening range.
