From every report and Dyno run I have seen, it would be fair to say that the Z1000 and the ZX9R are probably pretty equal in terms of power. Most sheets I have seen, seem to average out about the same for both. The 9 is lighter however so if gearing was the same one could naturally assume that the 9 has the advantage. Add ram air, and you have a little more top end advantage. (pretty much from 160kph on the ram air is passively supercharging the airbox.)
Now I have ridden both a ZX9 and a ZRX1200 up reefton spur. The ZRX was OK up to a point. This point was pretty much about the point where you have to start using a little body english on the 9 and not too much effort! Whereas at this pace the ZRX was frame flexing and wobbling all over the place. The one I rode was well wet up, but a Steel spine frame can't compete with a modern alloy beam cast, extruded, pressed and welded jobbie!
Engine wise the ZRX is probably one of the nicest big motors to ride with on the road. Torque and power was only a gentle roll of the wrist away and power was linear pretty much till run out of puff time at about 8000rpm. It made for a relaxing ride. But ground clearance is even worse than on a Z and nowhere near a 9! So it only takes two or three turns and the ZRX pilot is starting to have to wrestle it about like a proper Superbike of the 80's!

The brakes are great too! Ride Possie on the ZRX is awesome as is the Z for that matter, and for a sports bike the 9 cuts it just too. (Mind you a trip away on the beemer sure made the 9 seam little, cramped, hunched, nervous and twitchy, amazing what comparisons do.....)
If I were looking at these two bikes it would be hard to decide I reckon. The old school looks of the ELR ZRX1200 really appeal to a dinosaur of my ilk, but the Z has more modern Frame, Engine, Brakes, steeper geometry and more ground clearance as well as modern streetfighteresque looks. mmmmm It's a tough one, but the Z1000 would probably get my money if it was solo riding, but if a pillion were to be carried with any sort of regularity or distance, then I would definately opt for the ZRX!
I suppose the other real issue is what is available at what price when you are ready to buy too! That was small part of the decision to by that shitbox gearbox exploding BMW. It was on the market, it had the attributes I wanted in a tourer of shaft and panniers as min requirement and the price was right! Luckily the price was right enough to allow for the above mentioned exploding gearbox and still be happy!

"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?