Yeah, most of the mono builds I've seen have removing all of the linkages and welding a mount at the most significant point of the frame (varies depending on the frame, but people ususally go the front of the seat mount or behind. Doing all of that negates most everything you'd use one for. With a twin setup, you really can't go too wrong, as long as the shock angles don't become too extreme. It's the rising rate nature of using a longer arm with further back mounts (such as the DOHC arm on a SOHC 750) IMO that can make the handling feel funny. I like the stock rear geometry (but the rear swingarm flex can be a little iffy at the track) and have kept mine as is, but a little extension would be fine especially if you can get a nice box section aluminum arm for the effort.
Are you running a K? If so, that should handle really nicely, but watch for the neck angle, because the early frames have 27.17* of rake vs the later (@28.17*). With the gsxr frames, you loose some fork length, and unless you plan on dropping the rears, you're looking at an effective rake of a degree or two lower than the frame rake. 1 degree is probably fine, but 2 or more and you'll get a damn twitchy bike, especially if your tire is smaller than 25.5" nom D.
