I agree with the 400F exhaust looking better, but if you're trying to make a "sleeper", then 350 exhausts might be the way to go. The cases are immediately recognizable as 400F cases, especially the clutch, but the 350 seat, bars and tank all combine for a certain image and the 4-into-4 350 exhaust ties into that image perfectly. The 400F exhaust, while superior in look and function, would seem out of place, to me at least.
If I were making a shamless hybrid, I wouldn't hesitate to use the 400 exhaust, but since the 400 is a punched out 350 with better heads, it would be like a "factory" big-bore upgrade on a 350.