It sounds like the spark plug wires are out of order. You will need to be sure that the #1 cylinder is at the top of the compression stroke. At that point, known as top dead center(TDC), the rotor should be positioned directly at the #1 plug wire. From that point, going clockwise, the firing order is 1-5-3-6-2-4. Make sure the wires are in that order, or the engine will not run.
If you don't know how to find TDC, waldo53 has written a good method about half way down the page
HERE.
