I have both a 400 and a hybrid, both 3tjs. The handling is not noticeably affected as there is little overall wieght difference. The hybrid however does wheely a lot easier!
I have gone down the popular track of fitting the foxeye motor. I have also fitted an r6 rear shocker. The brakes, other than braided hoses remain standard and are more than adequate (will easily lift the rear under enthusiastic braking).
The 3tj fzr400rrsp's are quite rare and fetch good money, so I would look for a 3tj fzr400rr for the conversion (unless you found an sp at a good price) as the main performance advantage (as you are removing the engine) from the sp is the forks. The rr forks are adequate for the bike, i ran my hybrid on the rr forks with no ill effects untill i found a good set of sp forks .
Im currently in the process of building a new motor for my hybrid which will be 660cc. Im using the bottom end from the old 600 genesis and fitting the top end from the foxeye. The older 600 has a longer stroke + the foxeye/ thundercat have larger bores = 660cc. These barrels can also be bored out to 727cc as thunderbikesteve is doing. I will be posting a thread to tell all about the conversion when its on the way.

Thanks for your reply Tim, much appreciated, seems to back up what a couple of other members have suggested in my other thread. Look forward to seeing your progress, good luck with the build. The comment that handling is largely unaffected just seems to make this conversion all the more appealing. I can rember reading an article on a fella in Performance bikes some time ago about an Fzr hybrid bike with an R6 fairing fitted (marlborogh colours if memory serves me right) and being very impressed then. I think I just got caught up in the whole Honda V4 thing for too long and had the blinkers on abit.

I think that bike is fzrtim's it was on the PB 90's track evening last year.

I find a lot of honda owners are a bit caught up in themselves, ride the FZR standard and you'll find it more than a match for the 30 especially when consider the cost of them.

This is me!

I've gone down a lightly different route. I've put an FZR600 engine (the normal FZR600, not the Foxeye 600) into the FZR400R (3EN2).

I had her out on the roads for the first time yesterday and she handels just as well as she used to (maybe under very heavy riding she might flinch a little more, but didnt notice it yesterday)

Other than quite a huge dip at 5000rpm yesterday, she blew mt world. :)