Some 2 stroke Vipers were fast and some were not. If your 4 stroke Viper beats the 2 stroke one you have a slow 2s Viper. Mine was faster than heck and even with 9600 miles it could run neck and neck or beat most of the new stuff. I sold it at the end of 2013 and put every mile on it. On lake Gogebic I spun the speedo up to 125 mph one time. On GPS that was around 114 mph. On that lake I knocked off countless ZR800's, even a ZR900 , ZRT 600's and a 2 stroke Mach Z 1000 twin. My dad's was even faster than mine and was an F7 beater....yes the fast ones (2003).
All we had done to our two machines were Predator tracks and Heavy Hitter clutch kits.
I knew of other Vipers of that time which struggled with 600's. What you usually found was the fast ones had over 130 psi compression on the pto side and a good 145-150 psi in the middle and mag side. The slower ones had 110-115 psi in the pto side and around 125 psi in the other two.
Don't take this as a knock, just pointing out the big disparity between the old 2s Vipers performance. I sure put mine through the paces and when you have a machine that long you really get to know it.