My 1999 Honda shadow backfires on deceleration after steady throttle what could cause this? I have tuned it and cleaned the carb but it still does it.

Backfiring on deceleration is air getting into the exhaust and igniting unburned fuel. You probably have an after market exhaust on. You need to seal up the exhaust system by replacing all the exhaust gaskets. Dig the copper crush washers out of the head and replace them with new copper crush washers. This should take care of most of the popping. If the problem persists,unbolt the fuel cut diaphragms from the side of the carburetors and inspect them for holes and stickiness. Replace the fuel cut diaphragms if they are bad . Fuel cut diaphragms are on almost all Honda Kei Hin carburetors to stop the cycles from popping or backfiring on deceleration With the stock exhaust.

That is sometimes caused by leaking exhaust valves or air getting in to the intake manifold.

Back fire on coasting down,deceleration,is a lean condition,that will also cause the idle,low end sloppy throttle,idle speed jet has become dirty,a good carb clean/rebuild with carb kit,carburators synchronized,and fuel mix adjustment,I would also check for any air leaks,that can cause a lean condition too.

To help stop the popping replace the copper head o-rings and muffler to head pipe seals. Backfiring is typically caused by air leaking into the exhaust and igniting unburned gasses. Flickering lights indicate bad wire connections/grounds. Honda grounds the turn signals through the green wires. You will probably have to take off the seat and open up the headlight bucket. Try unplugging and replugging the orange,blue, and green wires going to all four turn signals. This should take poor contact and grounding out of the equation and sort out your flickering lights. Also go to the fuse box and take out the fuses one at a time and reinstall them. Make sure that the end caps of the fuses are not loose, if so, replace the fuse. Broken ar cracked fuses on older bikes can cause head scratching problems where there aren't any. Make sure that all your turn signals are grounded through the green wires.

Two things can cause popping or backfiring on deceleration. The most common is air leaking into the exhaust through the exhaust pipe copper o-ring gaskets. This typically happens when the exhaust is replaced without removing the old ones (doubled up) or simply reusing the old gaskets and they don't seal. The other thing that can cause popping is bad air cut diaphragms on the carburetors. If they are old and sticky or have holes in them they don't properly shut off the gas on deceleration causing the backfire.

Backfiring on deceleration is typically caused by carburetors that are out of sync. Having the carbs synchronized should improve or eliminate this.
As for the driveability issue at around 4,000 RPM; has the bike sat for more than a few months at any point? If so, the carbs could be partially plugged with gasoline varnish. Before doing a cleaning of them, try draining the float bowls. Sometimes a little moisture will collect in them and cause both backfiring and poor performance. Also, your bike uses "CV" or "Constant Velocity" carbs. These use a vacuum actuated rubber diaphram atop each carburetor throttle slide. Remove the four screws that attach the chrome cover to each carb top and carefully inspect the round rubber diaphram inside. If you see any sign of cracking - or holes - in the rubber, then you've found the problem.

I replaced spark plugs, filters, tightened boots, etc. Nothing worked. Then I dumped Sea Foam in the gas tank. 50 miles later...no more backfiring. I used 1 ounce per gallon. Get it at any auto parts store.