I bought an 03 FE 400 a few months back and I love it. Storming engine, top suspenders and it honks like an angry goose when you give it the berries!
The down sides for me:-
Finicky starter (likely particular to my bike). There is a definite knack to starting but even so mines been a PITA. I've been fidling with it and found that increasing the pilot jet has helped and setting the valve clearances helped a bit more.
Mine has a dellorto carb and by all acounts the Kehin FCR flatslide is better (37mm - 39mm I think). The delorto has an emusion tube or jet fitted (or not) above the pilot jet. Apparently some bike were not fitted with this and having it improves things.
I just got one and haven't fitted it yet so can't say what it does, but I'm hoping that it will eliminate a tendancy to bog and stall off a closed throttle. This coupled with poor starting has led to some frustrating rides but I reckon I'm on track to fixing it.
More frequent maintenance is a fact for any high performance four stroke so be prepared to spend time on the tools or have a good mechanic on good terms.
This site is an awesome resource.