If you had the water-cooled conversion done to your 350 (head, hoses, radiator, etc.), that would be a good thing because they are normally air-cooled. That in itself is a major difference between the 350 Odyssey and the 400 Pilot.
Another major difference is in the rear axles. On the 350, you have universal joints and on the 400 you have CV joints.
Finally, another major difference is in the suspension. On the 350, the rear is a swing-arm suspension and on the 400 it is an a-arm suspension.
As far as speed is concerned, I've heard on a couple of occasions that a hopped-up 350 will always beat a 400, due to a shorter stroke. I don't know about all of that, but I do know that they are fun machines, no matter which one you picked up!
Enjoy the new toy!!!