Having done a few valve adjusts myself, let me just add this ... it is easy to get the cam teeth off by one, especially as you think you have them lined up right before you tighten the cam holders, then the tightened cam holders change it by just a wee little bit ... and then off by a tooth. Been there, done that. Thus:
1. Take pictures of lined up cam markers before removing cam holders.
2. Always check cam alignment AGAIN after tightening the cam holders.
3. Spin the engine a couple times by hand. If it interferes, you'll know. If the cams are off, it will be easier to see.
On a Triumph Sprint (also interference) we did that, thought we had it all good, buttoned it up, started it, and it ran like crap with barley husks in it (i.e. rough). Pulled it apart, cams were off, put it together, now runs great.
Moral of the story: Not all interference engines break valves if off by a tooth, but it sure as hell runs like crap. Now we can add the FJR to that list. However, I'm surprised it didn't run rough.
I bet you couldn't let it rest until you figured it out!