What you need to know is camshaft rotation (as that is what the Boyer rotor is fixed to) so when viewed from the right hand side of the bike looking at the Boyer pickup the camshaft and Boyer rotor turns clockwise.
Are you sure you didn't re-connect the pickup wires the opposite way around, as that will throw the spark timing way off.
Did you use the correct alternator rotor mark when you re-set the timing? If you used the wrong mark then the sparks will be 180 degrees out.