How did you check the plugs for spark? On my 1997 1100 Spirit, I take one plug per cylinder and hold aginst the side of the cylinder while the engine is running. It should spark, if you take them both off at the same time, there will be no spark. If there is a spark, look for a plugged pilot jet in the carb for that cylinder.
1997 Shadow 1100 Spirit
K&N Air Filter
Cobra Slip-on mufflers
Cobra (DynoJet) Stage 1 Jet Kit