Well, he's certainly using Boss pedals in that Letterman video. The only obvious thing he's changed (other than his guitars) is his guitar tech. I'm not placing blame though as I don't know enough about when he got Takumi on board for his live performances after Lumpy left.

The fact is, you can make a sh*tty guitar sound good with a ton of expensive effects and decent backline but you can't make a great guitar sound good with a sh*tty backline and/or bad effects.

The guitars, as you said, aren't the problem here, it's his general tone that's suffered and my bet would be that chances are either his own personal tastes have changed or his new tech does things very differently. It's probably a combination of the two.