Thanks for the reply. I guess my description is too vague. I'm confident the boot is on correctly. The rear of the boot with the 4 tabs is the part I'm talking about. The tab on the top of the boot, closest to you when looking at it is pushed up against the frame and seems to inhibit the boot from seating properly in that corner. Does that tab need to be on the other side of the frame member (other side being closest to the rear wheel)? If the sun comes out today I'll try to snap a picture.
This might help you there are indexing notches in the end of the boot. take a close look at the photos and see if this helps.
JD
http://www.ebay.com/itm/86-KAWASAKI-ZG1000-ZG-1000-CONCOURS-DRIVE-SHAFT-BOOT-5050-/331115368863?pt=Motorcycles_Parts_Accessories&hash=item4d1803919f&vxp=mtr