Lowering - Vibration?
 

I've lowered my 650 1.5 inches using links. It may be my imagination but it seems there is more vibration now. Is is possible that lowering and a small adjustment to fork length (3/4 inch) could make a difference?

possible - the frequency of vibes could be different - everything vibrates at a particular frequency, and by changing the lengths of components you change the frequency - so yes, it's certainly possible that you feel it more. I'd ALSO check to make sure that when you moved things around, that you got the torque settings for all the bolts right, that nothing is touching a component that it shouldn't etc. Also check motor mount bolt and swing-arm bolt torque.

Vibration KLR650
 

Maybe you feel more comfortable on the bike and you are running it faster? Also I have noticed that even very small chages in attitude of the bike can alter the way the windshield dumps the wind on you causing a perceived buffet or vibration when riding. Loosen then tighten all of you motor mount bolts. I have come across more than one motor mount bolt that seemed tight but was just corroded in place. So by loosening and then retightening you get the correct torque.