It looks like the Wii U actually got adjusted up slightly in the period before July. So based on VGC/MC/Famitsu numbers, we have a pretty reliable number for Wii U units on shelves in Japan. That means the rest of the world outside of Japan only had ~19k Wii Us with 2 days left in the quarter according to VGC. Considering VGC shows the Wii U selling 58,145 outside of Japan in those two days plus the first 5 in July, it seems very unlikely that supplies were actually that low.
Also since I already have the numbers open, I think the 3DS got adjusted down a little bit, but probably not enough. The shipped sold gap in Japan makes up 75% of the overall Worldwide gap. I doubt there were less than two weeks of supply for countries outside of Japan at the end of the quarter.
I really don't get why these errors seem to persist for so long, and often get even worse.