I just wanted to share my solution to implement removable jumpers for JP1 and JP2.
As you can see in the attached images, I just used a 2x4 pin header installed in J3, and routed CPU's sides of JP1 and JP2 to the pins in parallel with 3.3V and GND of J3 with thin wires.
This way, if I install the jumpers the CPU enters the serial port flash mode, but without them, J3 (lower row) can still be used for its original purpose (serial wire debug). The upper row can be used to store the jumpers when not in use (as in the first photo).
As a suggestion, a future revision of the mainboard's PCB could include two extra pins at both sides of J3, routed to pins 20 and 44 of the MCU for the same purpose
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