Hmm strange looks like they removed the TP's. But it is pin 11 from flex connector (attached picture). Usually you shorten it to ground but could also be that you need to shorten it with another pin i dont realy know.
However you said gps were running yesterday for a short time. Hence I suggest an insulate contact.
So I would say it is realy a power problem or a clocking problem. Strace shows that the communication is ok until it should switch to operational mode.
Test the gps in a warmer enviroment. Place it for some minutes on the heater in your room.• Primary Power Control: via the specific Operational Mode message
(@@Oa Position Request Message).
• Low-Power: RAM and RTC are powered; 32 kHz is the clock source for
RTC; wake-up via combination of serial RXD/MOSI
activity, timer external signal; lowest power consumption
mode.
• CPU Power: RAM, RTC, and the ARM microprocessor are powered;
main power level for performing non-position activities;
clock source is synthesized from 32 kHz.
• Full Power: RAM, RTC, ARM, RF front-end, and GAM are powered;
clock source is 12-26 MHz host-supplied TCXO; used while
the positioning engine is executing.
You could also make some pressure on some parts and test if gps is working again. If yes maybe there could be a micro crack in some soldering.
For resoldering flip chips you need a hotflow repair system.
By the way did you measured some voltage? I saw you removed the rf shield nice.
In the "reference guide v2"/"Instant GPS Design guide" you find some voltages and at the end the circuits.
Attached picture is from "Sch_A780_A2_C_L3_1.0.pdf"



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