Motorcycle Repair: 1984 honda shadow misfire, jets air, honda shadow

Question
Ok so I bought this 1984 honda shadow ran great for 2days then wouldn't start got it start later that night it was running good and the started to bog and backfire and miss at 3000rpm I got it home let it sit over night ran good then started to do it again I cleaned the carbarator. Cleaned plugs inspected wires all good ran good for 2 more days then started again. Then I drained the fuel filled with premium fuel and the right amount of seafoam ran it hard let it sit till morning ran it hard again but it still back fires misses and bogs at 3000rpmafter about 9miles. When it acts up if I hold the clutch in or in neutral bit will rev and run fine but as soon as its in gear and gets to 3000frpm it does it again

Answer
Hi Steve,
It does sound like a carburetor issue. I understand you have cleaned the two carbs, it sounds like it's running lean. You did check/clean/replace the air filter? It may also take a bit longer than normal to return to idle when you close the throttle. You may get lucky and it is a fuel supply problem from the fuel tanks or plumbing instead of the carbs. (the 700 has two fuel tanks) If you don't have a service manual or the correct information to set the air bleed screws, float height, vacuum pistons (slides) and throttle plates (butterflies) you will be in for a lot of repeated assembly/dis-assembly most likely. If you haven't already cleaned them in this manner it may be in your best interest. Get a gallon can of carb dip/soak at an auto parts store and disassemble them completely. Soak all the metal parts and carb bodies for a couple of hours and then remove them, drain and blow the cleaner out of the parts with compressed air. Wash them down with spray carb cleaner or in a parts washer and blow them out again. Inspect them carefully for any foreign material, pay particular attention to the holes/passages in the body of the carbs and the brass jets/air bleed tubes, they must be clean. Don't put the vacuum pistons or other plastic/rubber parts in the dip, it may damage them. Inspect the vacuum piston diaphragms carefully for holes, tears etc. If they are damaged you will likely have to replace them.
You at minimum need a diagram of the carbs, you can look at one at the link below if it's the shadow 700, if not you will have to navigate to your model.

http://www.bikebandit.com/houseofmotorcycles/1984-honda-shadow-700-vt700c/o/m151

If your confident the carbs are clean and set correctly and the fuel supply is not the issue I would consider the ignition module next. It may be a bad connection somewhere in the electrical system, (grounds?) You can also try a spark tester like this one or similar. (http://www.bikebandit.com/bikemaster-ignition-spark-tester)
Connect it and see if the spark is consistent under load when it starts cutting out or the spark cuts out. It is also possible the ignition module or another component is bad. They are rather expensive from my experience. I am not sure as I haven't worked on many Honda electrical issues; Kawasaki is another matter, I am familiar with their electrical systems and ignition modules. They may or may not be similar to your Honda.
Regards,
Terry.