The airbox side OD is bigger, so an XR400 boot is needed:
One thing that is different, and still unresolved, is the crankcase venting. My bike is a California model, and had a more extensive crankcase recirc system. The 250 boot has a boss to attach the hoses to, that the 400 boot does not have.
Also, I noticed that the stock intake manifold had hardened considerably, so I took no chances and replaced it.