The Tone Board has a logic that determines SPDIF routing. Depends on whether the TB is used as a standalone or mounted to a VIM SBC.
After looking at the TB schematic’s SPDIF section, the junction between R56 and C113 is electrically the same as the SPDIF jack’s center pin. if you could connect a lead to that junction, the lead should function the same as the jack itself. In other words, as it did before your mod.
SPDIF input is available elsewhere, however, input elsewhere will be effected by the TB’s SPDIF switch logic and would require a workaround. that may be as simple as powering over GPIO as opposed to USB-C. I am not solid on this info regarding the SPDIF switch. I will try to study it further. The answer is in the schematic ref the switch logic.
One end of R56 is tied to ground, so it should be easy to determine which end of R56 to attach the lead. Junction of R56 and C113 indicated here…
For component locations, see the TB silk…
As you have found out, caution needs to be adequate to prevent damaging the PCB. These boards, like most modern PCBs, can be easy to damage with excessive heat, or attempting to lift a component who’s solder is not fully molten.
Good luck. Keep us posted.