Regarding second gear: If you are experiencing the following symptoms:
*The bike produces a jerking sensation which occurs only in one (or only in certain) gear
*The jerking occurs only above a given load level (if you use less power, it stops, if you use more, it gets worse)
*The feeling is like it briefly jumps out of gear and immediately back in, but in a repeated cycle.
...You are most probably dealing with a set of worn locking lugs (aka "dogs"). In the case of second gear on the FJR< these will be in/on the second gear "wheel" (output shaft gear) and the 5th "wheel" (also on the output shaft). These are normally very slightly undercut so the gears "hold in" under a load, but when the undercut of the lug wears and becomes reversed, they push away from each other instead, deflecting the shift fork until they disengage, then, with the load temporarily gone, the fork springs back and re-engages them. Then the do it again. The fork will be damaged by this, so don't neglect replacing it as well.