I raced a 2003 ZX6R 636 for 2 years, switched to a 2004 ZX6RR for one race and went back to my 03 636.I knew there was going to be a difference in power and torque, but I couldn't believe how much.Both bikes had all the same performance parts on, but the 636 had a lot more punch out the corners and the power didn't drop off untill it hit the limiter. The 6RR though had less punch out the corners and the power dropped off sharply after 14000 or 14500 rpm. The slipper clutch was nice though.The more adjustable chassis, adjustable swingarm, are only needed for factory teams that really want to get the last bit out of the handling.Even if you do make the bike handle better, it wont make up for the motor.I was more than 1.3 seconds slower on the 6RR than the 636.
I have now sold my 03 636 and bought a accident damaged 06 636. Out of all the ZX6's I've ridden this one is definately the best. In 3 days I was within half a second of my best time on my 03 and the bike is basically still stock. The chassis is a major improvement over the 03/04. The handling stock is better than my 03 which had a front internal kit and a WP race rear shock. It makes it a lot easier to do the times. The stock motor is nearly as strong as my 03 636 which had a filter, velocity stacks and a full Akrapovic race system. For my next race I hope to have my new Akro full race system which should save me about 5kg and add a bit of power.
Everybody said the 05/06 handles better and they were right. I really liked the 03, but after just 1 race I'm very glad I got the 06.
Coming back to your question, the 03 636 is definately better on the track than the 03 6RR.