Regarding shorting out pins, I wonder what 5 volts down the input pins of the USB Controller chip would do.
Nothing interesting in principle, though I haven't had an opportunity to test it in real life yet
Universal Serial Bus Specification Revision 2.0, 7.1.1 USB Driver Characteristics, page 124
A USB transceiver is required to withstand a continuous short circuit of D+ and/or D- to VBUS, GND, other data
line, or the cable shield at the connector, for a minimum of 24 hours without degradation. It is recommended
that transceivers be designed so as to withstand such short circuits indefinitely. The device must not be damaged
under this short circuit condition when transmitting 50% of the time and receiving 50% of the time (in all
supported speeds). The transmit phase consists of a symmetrical signal that toggles between drive high and
drive low. This requirement must be met for max value of VBUS (5.25 V).
I will tell you what happened: the previous owner knocked these components off the board while trying to replace the USB connector. Or maybe desoldered them and couldn't put them back. Or lost them, or broke them during desoldering.
Either that or he managed to apply mains voltage to the USB input. But there are no smoke stains.
As for the data lines, I bet they go straight through L5 to U4. L5 was a common mode choke to suppress EMI, the device will work without it (replace with two straight wires). Then you may look for a proper replacement, but I am not familiar with that stuff.
The only serious problem is the mayhem around U38. You need to identify it. It doesn't look like a switching regulator, because there is no coil in the vicinity.
edit
Trace how things are connected around U38 and U39 and post a schematic.
That guy from Poland has 47kΩ at R51. Both he and the Brazilian have nothing at C139.
Is your U38 visibly broken or only disconnected from the board?