Wheelbase will alter with head angle and swingarm angle as you know. I wouldn't worry too much if it ends up at 54-56 inches.
I hear you about some sag when you sit on it, but the starting point is so far away from useable though. Might I suggest that you take a good look at say a stock SV650 for comparison and maybe say a MotoGP bike which lives at the edge of total instability. The shock mounts will have to be changed or find a shorter shock assembly.
Here's a link to someone looking at the same issues. http://pinkpossum.com/GT750/phattrakka/part4a.htm
edit: I went back a page or two and see where you took a wrong turn that is causing the current issues. That shock is designed and valved and sprung to work with a linkage and the linkage would in turn have allowed a better swingarm angle. If the stock SV linkage mount is still on the lower side of the swingarm, you can probably pick up a linkage arm cheaply and then month the lower end of the link to the lower rear frame rail. I suspect that will bring things back into alignment.
It will also allow the frame to rotate backwards to an angle that is a lot closer for the steering head.
I hear you about some sag when you sit on it, but the starting point is so far away from useable though. Might I suggest that you take a good look at say a stock SV650 for comparison and maybe say a MotoGP bike which lives at the edge of total instability. The shock mounts will have to be changed or find a shorter shock assembly.
Here's a link to someone looking at the same issues. http://pinkpossum.com/GT750/phattrakka/part4a.htm
edit: I went back a page or two and see where you took a wrong turn that is causing the current issues. That shock is designed and valved and sprung to work with a linkage and the linkage would in turn have allowed a better swingarm angle. If the stock SV linkage mount is still on the lower side of the swingarm, you can probably pick up a linkage arm cheaply and then month the lower end of the link to the lower rear frame rail. I suspect that will bring things back into alignment.
It will also allow the frame to rotate backwards to an angle that is a lot closer for the steering head.