1) Getting the lower race off the bottom triple tree when replacing the bearings (upgrade to the super sweet All-Balls Tapered bearings) is a complete pain in the ass.
2) Those o-rings on the coolant pipe that goes into your valve cover. Those that look like they are in really good shape? Yeah those, replace them anyway. Trust me on this. I didn't listen to this advice and got to do this part twice.
3) Double, and tripple check the valve cover gasket. Do it before you put in all the bolts, and install 3 spark plugs. I check once, but not twice, and got to do this twice too.
4) Engine Error code #21 means you forgot to plug the temperature sensor back in.
5) It really does help to put all the nuts/bolts/screws into separate containers, so items for each panel are grouped together. It really cuts down on the WTF does this go questions.
6) Having actual metric feeler gauges saves a lot of unnecessary math.
Other than that, the project went well. 33k miles, no shims needed to be replaced, and no parts were left over or lost.
http://www.dishers.com/2009/06/01/fjr-33000-mile-maintenance