Both are hell fast. The 600 is going to eat a few less tyres and a few less litres of fuel. It will also sell faster when the time comes. It is lighter, easier to turn and easier to hang onto for a few laps.
The 1000 is going to be harder on you physically. Harder to turn it, harder to control it and harder to get the most out of it. On the flip side, litre bikes are some serious giggles on a track. You can play with the throttle and have some fun opposite locking it out of turns

, wheelstanding it, smoking it!!
I'd probably opt for a litre bike. But, I have had a shed full of 600's over the years and even spent a few years punting them on racetracks. So for me, the litre bike is where it's at. (Not to say I wouldn't have a 600 trackie if circumstances presented themselves....+ I already have a 600cc racebike....all be it an older one...1996) But the 1000 would be my preference.

"I hate to advocate drugs, alcohol, violence or insanity to anyone, but they've always worked for me" Hunter S. Thompson.
There are really only two questions in life. 1.Which way do i go? 2.What is the lap record?