"If you plug a USB stick into an infected machine, that gets the pox too." Yeah, but you can't get "the pox" from the USB stick (unless you manually run it from there), because autoplay doesn't work for USB drives.
Trojans don't "spread". If something can replicate itself, it is a virus - not a Trojan.
"By comparison, the Storm worm was removed from under 350,000 machines in the first month that detection was added to MSRT." Yeah, but the Storm family of Trojans (it's not a worm) uses server-side polymorphism - meaning that just about every instance of it is a different variant. There is no guarantee that the Tool has found them all - in fact, it most likely hasn't, thus the lower numbers.