I checked FB1 and both sides are not shorted.
not shorted in reference to ground? or between both sides?
In the tracking red lines I mark each side of FB1.
one of your lines goes thru a cap to the ground, while both usb signals go thru fb1, it has 4 pins, and should pass signals
and the signal can be seen at the microcontroller pins.
wait, what signal? your scope cant capture so there is no way of you knowing if there ever was an attempt at handshaking
if you cant get a scope able to sample at ~2MHz and capture on trigger and your desperate enough you could desolder U3, C18/19, FB1 and jumper over it.
I hope you checked with different usb cable already