Check this out...same problem, bad cam.
http://www.riverracer.net/forums/archive/index.php/t-75550.html
same issues when I first purchased boat with stock engine.Engine in boat now is almost entire differ setup,only things the same from stock boat to now is fuel tank,thermostat housing,and, alternator and distributor.
3: Backfires Through Carburetor (From Mikuni Corporation website)
Common Causes:
Ignition: The engine's faulty ignition can contribute to backfiring through the carburetor.
Cam design: Long duration cams with early opening intake valves can contribute to backfiring.
Intake manifold air leak: A lean condition due to an intake manifold air leak can cause backfiring.
Carburetor jetting: An overly-lean low-speed circuit, non-functioning accelerator pump or clogged pilot jet can contribute to backfiring.
(Backfiring, defined)
When starting an engine, timing that is too advanced will fire the spark plug before the intake valve is closed. The flame front will travel back in to the intake manifold, igniting all of that air and fuel as well. The resulting explosion then travels out of the carburetor and air cleaner. A common air filter will allow the gases to escape, but will block the flame front. On many small marine engines, no air filter is used, but a screen is placed over the intake of the carburetor as a flame arrestor to prevent these flames from escaping the intake, and potentially igniting fuel, or fuel vapors in the enclosed sump or bilge of the boat and causing a fire or explosion. Improperly adjusted carburetors that create a lean condition during acceleration can cause the air fuel mixture to burn so slowly, that combustion is still taking place during the exhaust stroke, and even when the intake valve opens. The flame front can then travel up the intake and cause a backfire. In this situation it is conceivable that there is a backfire occurring in the intake manifold and exhaust manifold simultaneously.
Here's another one...
http://www.carkb.com/Uwe/Forum.aspx...does-vacuum-leak-causes-backfire-through-carb
And yet one more...
http://forums.corral.net/forums/5-0-5-8-engine-tech/877054-popping-through-carb.html
The only reason I have not agreed with the lean carb issue is that you have already tried more than two carbs, and have redone the entire fuel system. Vacuum leaks could still be a culprit, and as I have said, timing (be it from the chain, all the way to the dist). Like the other s have said...throw a crapload of fuel in it, and if it stops...its a lean condition. If it blows up, it was timing.