so yes you have a quartz, it is the metal can next to the controler, but by now you have bigger problems, what seem strange is having something burn up on usb, it is so current limited that it should not really be able to, at least if the pc is respecting spec, same for the sparks...
and for next time, there are 2 vss on the chip, one is much further away
and anyway it was dead you are trying to fix it, can't really get worse
as long as your pc isn't dead that is.
so where was the smoke coming from? if it was from the controller then it is pretty much guaranteed it is dead, although any usb compliant device should support a short from dataline to vbus (D-/+ to VCC or VSS). otherwise i would guess it is a resistor or diode somewhere else that did not like that, still going to need replacement but may not even prevent the board from working depending on the failure, and is cheap and easy to find.
i forgot you said you did not know how to use a multimeter so i did not warn about anything... sorry.
-in voltage mode (V) you can probe across anything (low voltage if you have a cheap meter, or low experience, and care for your life) the meter will not short anything
-in current mode (A) if you put the meter across 2 connection it will act as a short, and measure the current going through itself
-in resistance mode (Ω) the meter will act as a power supply and will measure the current across what you are measuring, it will also act as a short in some ways, this mode should not be used on powered electronics, while the other 2 are useless without power.
as per your water damage i was trying to describe a very bad case of oxidation on a pcb, the parts at the bottom should only affect the switches if anything, in the other hand it seems like the water damage near the chip is only on the ground plane (huge copper areas) and should not affect anything but is awfully close to the D+ pin, and it that pin is too oxidized it would prevent communication with the pc.
hopefully your board is reasonably fixable. good luck