I did a complete top end and wiring overhaul of the bike.  I'm not done with my harness yet, but I wanted to see if the engine would turn over.  I can turn the crankshaft with a wrench on the timing rotor and everything seems to be aligned alright but I jumped the starter and it wont turn over.  I hooked up car jumper cables to the battery (running at 12.5 volts) and tried grounding the cable on both the frame and the motor.  When I touched the lead to the starter there were sparks from the alligator clips, as expected, but the starter doesn't move the motor at all.  

Is there something fundamentally wrong with the way I did this or do I need to investigate the starter gears?

You've stalled the starter on the compression stroke.

You should be able to put it in gear and back the bike up to turn the engine over to the compression stroke.  Then when you get back to the compression stroke the starter and engine already turning will have enough momentum to get thru the compression stroke.