Wilsons Sandbox

I have a KLR600 that i've been restoring, and finally got round to sorting out the valve clearances after buying a shim kit. The clearances are now all within tolerance, but not really how i would like them to be. ie the 2 inlets are at opposite ends of the tolerance scale, as are the 2 outlets! How much difference will this make? I had hoped that the clearances were the cause of a bad vibration, which builds as the revs go up. It sounds like it is coming from the cam case. There is a contraption on the end of the exhaust cam shaft. What is it? There wasn't one on the engine I stripped down, but i never heard that one running. I mentioned before that the cams do not line up with each other at TDC. The inlet cam is perfect, but the exhaust is slightly advanced, by less than half a tooth. I can't see any way of adjusting this. Can anyone give me any clues as to what may cause the vibration? Charlie