Your other bike is also taller because it's built in a totally different manner for a totally different purpose. Are you dragging hard parts when riding aggressively? The bike is sprung for a 140 pound Japanese guy. I don't know how much you weigh, but most of us here are certainly not that small. The front springs have a rate of .39, many of us running other springs are running .9-1.2 depending on weight. The damping in the shocks is also not that great.
You may also want to consider the face that your R1 has a tranverse mounted motor, different exhaust routing, frame material/geometry/concept... pretty much everything except the fact that it has two wheels and some lights on it. There's also a lot more weight on the front, so it feels so much more controllable. There are a lot more things other than ride height that need to be changed to get a V-Max to handle the way it seems you want it to.
If you just want to change the geometry, look for some ZRX1200 shocks and lower the front an inch, either internally or by sliding the tubes up in the trees. Sorry if this is pretty much what I said earlier. I just know the feeling of going sport bike-> V-max.