you're covering two different generations of motors there - the 92-95 water pumpers and the 96-99 srad motors.
the 92-95 motors would go in a lot easier in a 91 chassis, than the 96-99 mills. the 96-99 motors are a completely different configuration than previous gsxr's, with the cylinder bank angled a lot more forwards, the use of downdraft heads, different mounting points, etc.
to add to Jeff comments.....the SRAD suspension, frame, wheels, brakes and possible mod upgrades are light years ahead of the oil cooled stuff. If you have an SRAD motor, put it in an SRAD frame......I know I know. I have had 3 gixxers (88, 90, 92) and will but another when my 88 is done. but next year I put an end to the streak and get the '02 600.
If you have to stay with the oil cooled stuff, then get Tele forks (89 are best and lightest) Marchesini wheels, 36mm flatslide carbs and full duplex yosh exhaust and take off every steel bracket and replace it with Carbon or aluminum. That bike will be about 400 lbs wet and get you as close to an SRAD as possible.