I guess you answered your own question.
The orientation of the capacitors is different so you can't use a V1 cable on a V2 Switch.
Unless you want to use some wires to but then you might as well connect the wires directly to the picofly board.
Refer to the picofly manual on which capacitors to connect to.
This is to help install the PicoFly hardware mod on any and all Nintendo Switches
The green wire is just the GND. Note that the original manual assumes you have a flex cable with mosfets but most new boards have the mosfets on the board itself.