First thing I would suggest you do is run a compression test on the engine. That will allow you to eliminate poor exhaust valve seal or bad rings as a factor.
Next I would check the electrical power side of the equation by checking the voltage at the battery with the bike running. If your not seeing at least 11.5 volts, start checking for a bad ground somewhere, poor alternator output, or a bad voltage regulator. My hunch is that your problem may be a weak spark and low voltage will cause this. One way of confirming a weak spark issue is to see if the problem is worse at near full throttle because as the charge pressure increases a stronger spark is required for reliable ignition. A weak spark will also become more of a problem as RPM's increase due to coil saturation.
Many years ago I had a 1974 CB450 and it had a single throw crankshaft and fired both spark plugs at once. My current bike is a 1983 V45 Sabre and it's uses a similar scheme with the front bank firing the plugs as a unit and the rear bank firing as a unit. So, with paired cylinders, it is standard practice for Honda to fire both plugs at once. An easy way to see if you have a single throw crankshaft is by putting one cylinder at TDC and then checking the piston position on both cylinder using a probe in the spark plug holes.
If the cylinders are paired, it requires a lot more power from the electrical system so it's important to make sure it's up to the task. Honda also uses a VERY basic and somewhat cheezy voltage regulator on these bikes so it's not unusual to have one get weak.
Finally, you'll also want to check the color of a newly installed set of spark plugs. What you want to see is a light tan color after a short moderate power ride. If they are black with soot, your carburation is rich, if it's dead white, your running lean. Both issues require correction although running rich isn't as harmful as running lean. Chamber temps when running lean can get high enough to melt a piston on a sustained ride, so if your running lean, get that corrected ASAP. Unfortunately, you'll probably have to fix that miss before you can get an accurate plug reading because a missing engine will almost always read rich due to the raw gas being run through the cylinder.
PS, when I restored my Sabre in 1999 I stripped the wiring harness from the frame and sandblasted every single connector. Then, when I put the bike back together I used silicone dielectric grease on every one of those connectors. While it took a bit of time to do this, it's saved me countless hours of trying to track down an electical gremlin. In a worst case scenerio, you may have to do the same thing because all it takes is one hidden corroded connector to have you contemplating dynamite.