1980 KZ440 Bike bogs at higher speeds

So I picked up a cheap KZ440 a couple weeks ago. It's my first bike. The previous owner had removed the air box and put on cheap pods, but he had never rejetted the carbs. The carbs were also in pretty rough shape, so I rebuilt them and cleaned them up as best I could. The exhaust is a 2 into 1 that dumps through a muffler on the underside of the bike. I've got the bike running, and it's drivable below 45 MPH, though it does seem to be running fairly rough and weak. Once you try going above 45 MPH, it starts to bog bad. Is that typical behavior for a KZ440 without the air box, or should it be more drivable than what I'm getting right now?

I'm planning on fabbing up a manifold and doing a single carb conversion, but I want to make sure I'm not going to be wasting time doing all this for an engine that's got other serious problem. If the missing air box isn't likely the only culprit, what else should I be looking at?

My base timing is set correctly, but my timing light only strobes at idle RPMs. If I throttle up at all it stops flashing, so I've been unable to check if my advancer is working right. Would a bad advancer lead to the problems I'm getting? And why would a timing light stop strobing at higher RPMs? Could that be a sign of a bad coil, and could that lead to bogging at higher speeds? Thanks.