Of the two bikes, I'd say the Honda is better in stock form and it has more potential. It is faster and will handle much better than a Raptor 350. The Raptor 350 is just an updated warrior and those things are pretty slow. On the other hand the Raptor is a better looking bike. If you plan to drag race, I think a Banshee is the best way to go, you can't touch a well modded Banshee with any 4-stroke unless you put a turbocharger on it.
Both are about equal in power and speed the 400ex has got a little on it but not much. 400ex is a wheelie machine due to its motor being set further back. Both engines are pretty much bullet proof with little to no flaws in either engine they have both been around for along time. The raptors older brother the warrior was the best selling sport quad for many years. Both motors are old air cooled technology but run like a fully wound clock.. If your looking at the 400's id go with a KFX/Z/DVX (all the same quad just different names) Stay away from the 03's unless you are a good welder and can gusset the frame.... Any questions or anything i didn't answer please feel free to ask me or check out the forums. Oh both are superior trail quads but the 400ex has the lack of reverse which comes in handy on the trails. Ride on