I gotta' go with the suggestion that Kirby made.
Check those mounts, and then pull the cam plate, and check the pinion run-out, and not for nothing, pull the outer primary cover and take a peak at the sprocket shaft.
You'll have a good amount of diagnostic info at that point.
Scott

 

Crank runout and gear drive cams don't get along too well. This is what happened when my wheels slipped.

 

The vibration is why I changed the front mount. It is still the same. The front mount is tight along with front stabilizer, and the top mount is tights also.
Checked fall away today and it is ok. Just a little tight but I believe it's due to all the wiring in the bat wing faring, your can hear it squeaking when at full right lock.

 

Time to check runout.

 

I also have an 03 that was idling and running so rough everyone thought my crank slipped. I put in a new front mount but had to go back and center it after I installed new rear rubber doughnuts. They are 43 bucks and you can install in an afternoon easy. All of my friends originals went bad at 20 to 25 thousand. It is a well known problem. The new rubber doughnuts and mounts are stiffer and thicker. To center the front mount loosen the two side bolts on the front mount and the center bolt. With the bike straight up and down, off the side stand start bike and let idle for a minute or so reving it up a little helps. After this procedure my bike feels like new, very smooth even with big bore 95 kit. BTW disregard advice to visually check mounts. Not all front mounts rip or tear so badly that you can see it. Mine looked like new but were actually JUNK. The rubber doughnuts are not visible untill 'you remove them. They compress from axial pressure from the swingarm compressing them so they get thinner and sloppier and don't dampen effectively. The purpose of centering the front mount is to eliminate any side load on center bolt which transmits vibrations to the frame. Next step is to check and replace cracked inner stereo mounts on bat wing, another almost universal problem when engine mounts go bad causing vibration in bars. Harley and aftermarket has reinforced replacements available. Have fixed vibration problems on many Road Kings and E Glides. Nobody has had bent cranks in our group yet. Statistically a rare event according to several indy mechanics as well as dealers I've talked to. I do know one guy who sent his crank out to dark horse and after reassembly problem still there. Great excuse to go bigger though. If after replacement you still have trouble than check runout but remember you will have to replace the mounts anyway as your bike will develop a case of the "wobblies " as your mounts fatigue anyways and I bet it already has anyway.