Timing problem, 97 Speedster 717, can't figure it out!

[gslewis30]

Since I bought the boat last summer one motor has always been misfiring. I had the carbs cleaned, new plugs, new fuel, oil, filters, etc. I just rebuild the motor this spring and double checked the stator/magnito alignment and rotary valve alignment. I got a new ignition coil and the motor STILL misfires. Its hard to start and backfires back into the carb. I checked the timing via PTO wheel and found out the motor is firing when the back piston is halfway back down the jug, not at TDC or even close, (i.e. timing mark is more than 3 inches off). What could be causing this drastic mis-alignment?

Any ideas?

Thanks

Greg