Interesting. I am having the same problems on my 2001 Fatboy. Cranks, gets fuel, but no spark. Was thinking coil. Might try getting a new sensor.

 

Check crank sensor....Possible failure...usually causes no start ?? Just a thought...Have a great day.
TOOLBOX

 

The crank position sensor works off the "hall effect" senses the the teeth on the flywheel and when an empty spot shows up it sends a signal to the ignition module, then to coil and produces the spark. Wish I had seen this post a little sooner could have helped you out. During oil changes an errant oil filter wrench can reek havoc on this sensor.