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Just use the little square pad right at the Mic Mute button, it's easier than using the via for it. The Create and Option buttons are the same way and have that square pad at their buttons also, I just marked the via for them as it's close to them, the via for the MM button isn't near it.
Yup, that's it. It's an active Lo button and the DS5 logic is 1.8v, so if you're interfacing it with some chip it's best if it runs at that voltage.
The DA9087 does nothing with the USB data lines, it does the Power Management and Trigger motors. Those lines measure around 1.4M to ground here, so that 1.6M seems fine, but that 11.7k is no good at all. Make sure the USB connector isn't full of something conductive, but aside from that about the only thing left is the MCU.
It's an Inductor, no idea on the value, and it's on the 5v line from the Expansion port. Even with it missing the controller would still function and charge normally over USB, it would just not charge when placed in a dock. If it's not charging over USB, then when someone blew that thing up then they most likely fried the PMIC in there as well, the DA69087 chip.