Check your compression, for sure. If one cylinder is/was lower than the others by more than 10 PSI, and then the carbs were vacuum balanced on top of that, then that cylinder will spit back into the intake tract on every revolution.
The pipe will not affect your jetting significantly until 6000+ RPM, but the air filter can: what type of filter did you install? For the jetting issue at high RPM, try adjusting the jet needle's clip (move the needle a notch up), but NOT until you've verified the compression, or it will just cause confusion.
If the intake valve(s) is leaking, this will cause the symptoms you describe. This leak can come from a crudded-up valve, a burned valve, or a worn-out valve guide that doesn't let the valve seal quickly when the cam closes it. If you suspect dirty valves or worn guides, then increase the valve lash clearance to .004" to .005" and run that way for a while to see if things start to improve. If you suspect cruddy valve faces (often caused from sitting for long periods of time, as the valve sat open to moist air over time), then you can try an old trick, which helps clean them: first, remove the airbox (so you can access the openings of the carbs) and run the engine for a good long time to heat it up (30 minutes or more). Then, with it running, squirt in some water to one cylinder at a time, holding the engine at 2000-3000 RPM as steadily as you can. It only takes one or two squirts, less than 1/2 ounce total water, to shock the valve face and make it release the bits that might be stuck to it. Easy to say: hard to do! I've used a detergent bottle (small one) to squirt the water, still is hard to get it in. Don't make it real big squirts, as this can hydraulically lock the cylinder, instantly killing the engine:that can be real hard on the pistons, even rods. Some folks have done it with a squirt gun, but this isn't much water so it doesn't always work out very well.
If all else fails, get a top end gasket kit and pull off the head, and take a look: leaking valves will appear clean around their edges where the gases are moving back & forth (instead of one direction), which slowly washes off the carbon coating.