They are similar in speed and personal preference which one is "better." The Z is more technologically advanced, with reverse on all years, twin cam liquid cooled motor and rezzies on front shocks on 05+ models. 2009+ models have EFI. There are also Kawasaki (KFX 400) and Arctic Cat (DVX 400) versions also made by Suzuki. I think the 'Cat version looks the best.
I had friends that had 400ex's years back in the pre 450 era and they really liked them. I never owned one myself. I did own a KFX 400 for 8 years with no issues other than regular maintenance. Only sold it to get a Kawi 450R.
I've owned both and in stock form the Suzuki will be faster in a straight drag race. When I had my 400EX, mine had an aftermarket exhaust, air filter, 4 1" holes drilled in the lid of the air box, and was rejetted. A friend of mine owned a Suzuki and even with switching riders the Suzuki was faster. One the track, they're very comparable in handling, I personally prefered my EX on the track. The Suzuki felt more peppy coming out of the corners than the 400EX did, though.
No such thing as boring over 20cc's. Its more than likely bored over 20 thousandths of an inch. Which will make zero difference from stock in power. Your big bore options are 416, 426, 440 and those could be measured in cc's but they are bored in millimeters. Stock is 85. Yours is most likely a 85.5. 416 is a 87mm. 426 is a 88mm. And a 440 is a 89mm.
My 416 destroyed every z400 it has encountered. One of my friends has a stock bore high compression Z with oversized valves, high rev springs, and large cams and i walk away from him like hes standing still. When i ride his it does feel like its geared lower and pulls harder out of tight corners. The big difference is your 400ex will always beat the z400 in the long run. His will need rebuilt regularly and when his is down you will still be riding yours. My .02