Usually you want to keep the carb above the exhaust. That should produce the most reliable idle for landing and taxi. With a pump carb however, it is not required, but it sure won't hurt either. There is nothing wrong with mounting the engine sideways and having the carb on top. Most of the twins are arranged this way. The cooling would be excellent if you used baffles.

As far as balance goes, this would not upset the aircraft in a major way. I would avoid using wing tip wieghts however. This would cause the moment of the wieght to be far outside the center of gravity. Having wieght this far outboard will affect roll characteristics. I would strive to use the wieght you have in batteries (reciever and ignition) and other gear to attempt to offset any imbalance the cylinder head might cause.

Chuck