IME the first things to interfere with swingarm down travel is the dogbone against the exhaust (varies by what type of pipe), and the chain guard mount boss against the L peg mount.
The ONLY thing that can change ride height other than major mods to the cushion or swing arm linkage mounts or the swingarm pivot (highly unlikely) is the shock, and the linkage itself. I once bought a 4th gen track bike project from a member here, and in the pile of parts was a variety of traingles, and dogbones from many different Hondas. Some appeared to be identical, but if fact were slightly different. The nature of the linkage on the the VFR is it takes very little to make a large difference in ride height.
I would double check all your bolt to bolt measurements on the linkage to be sure.