The whole thing is strange and difficult to diagnose remotely. If it helps at all, my gear lever has lots of play in it, even after replacing the pivot bolt in the foot rest. I don't have any issues like yours although shifting has become a little less smooth after fitting the foot peg lowering kit. This is because the distance between the peg and the lever is reduced because of the lowering. The difference in angle is what's making the shifting feel "stiffer", a long lever could alleviate it, but it's very difficult getting a longer lever for a Wee that doesn't cost an arm and a leg. I'll have to remove the foot peg lowering kit because of this as I also can't adjust the lever so it is high enough for my off road boots now (lever hits the bottom of the foot peg hanger bracket before it's high enough to get the boots in under it, only just though.) I guess the whole peg lowering thing doesn't help you, but the just is that the angle of the linkages could affect things. I believe you've checked these already so it might not be of any help.
