You scared me and I'm glad you did. I just so happen to be in the process of adding bigger carbs to my combo. My new Mikuni VM32mm carbs would not go through the full travel. They either wouldn't open all the way or wouldn't bottom out.
I ended up deleting the loc nut on the carb cabs and used loctite there instead. This gave me full travel.
There is also another loc nut on the handlebars just before the thumber. There is also a throttle stop inside the box that could be ground down for another few MM's of travel.
I don't see a reason why the 400ex thumber couldn't be used with up to a 35mm carb- 39's might be a stretch.
Here's a pic of the stop and upper loc nut that could be deleted for more travel.