As long as V2 is created on the main pcb (R19 & R20), and the switches for MOS, SW and FCV physically connect to the main pcb then your circuit is complete and all you need a 3PDT board for effect on or bypass. You don’t mention pcb3 or pcb4 so i don’t know what the fancy switching is for.

Ok I checked this out at Tayda. The three wire connection is the boost on/off switch which is a footswitch in your case. The 4 wire connection is labeled on the board, as you said, and goes to the corresponding pad on the FS board. I can’t see where the current limiting resistor is mounted on that FS board but do not forget to use one between 2.2K and 4.7K. The other pads will wire according to their labels for in out and power and ground. Just a note that the power is input at this board and then wired to the main pcb. The footswitches should probably trade sides of the enclosure so that the 4 wires can reach the FS board. I see no reason for a 6 to 7 jumper as the boost switch will use a single column of the switch as a simple yes/no. Choose 1,2,3 or whichever. The second schematic that you attached is for a board you are not using that Tayda offers. Disregard it. A little ingenuity could factor in a led for that boost action if you wanted. Possibly what the 6,7 jumper is about. I’m not used to their methods. I’m all about Barry’s boards and methods.

I might be able to simplify if further. your boost is switched on and off by making a connection between either the yellow and red  or yellow and black wires from the 3 pin connector. you can try to manually connect them to verify the boost is switching on and off and working as expected. If that’s good, then wire the stomp switch accordingly. yellow on a middle pole and red and black on the corresponding throws. use an ohm meter to verify you have it oriented correctly.

Thanks for the pics. At a very minimum you need a way to check continuity to create diy pedals. You really should have a digital multimeter, an audio probe and a way to use it effectively, and a tone generator so that you can input tone without plucking guitar strings as you troubleshoot. Troubleshooting will happen. Nobody gets it right 100% of the time. Its great to ask questions but you need a way to verify. The schematic provides you all the info you need for an accurate and performing circuit. The bypass switching is not shown and is assumed as with very many schematics. Its unfortunate that the 3 and 4 wire connectors use the same colors. Its confusing because red and black are often reserved for power and ground connections. For the 4 wire connector red and black are +volts and ground. You should be able to verify that with a continuity checker by touching one lead to the + pad and the other lead to the collectors of each of Q1, Q2, D4, C13 or R19 according to the schematic. The GND pad should have continuity with every shown ground on the schematic. V2 spots should all connect and be provable. Very important so far. White is IN and yellow is OUT. IN should have continuity with R1, C1 and C2. Out should have continuity with C12 and R18. These are all clearly shown on the schematic and MUST be correct. Those should go to the 3PDT board as agreed earlier. They do but this is where some things go wrong for you. That switch is NOT the boost switch as you say. That switch and board are for Effect on/off, Bypass and led. Everything brd said above is correct. The 3 wire connector is Boost. Prove it. Easy. Don’t switch wires around. Yellow should have continuity with pad2 of Drive and C5, which means it is the middle position of the switch (whether its a toggle or stomp or whatever). Check me. Check continuity according to the schematic. Lets pick R8 because it touches everything boost. On one side, the pad to R8 should have continuity with pad 2 of the boost control, and an outside position of the SW (boost) switch pads, and on the other R8 the pad should have continuity with position 3 of the FCVA switch, C6, C4 and pin 2 of U1. Easy to see on the schematic. Prove it to yourself. Omit any boost led for now and any other mods to the original until you get a working pedal would be good advice. Then mod and test one thing at a time for best results. Sounds like your pedal mostly works but you are not sure how. For sure the way you labeled the switches is opposite. Every line on the schematic either exists as a trace on the board or it is a wire to be placed by you. Intersection points may only exist on the schematic to make it easier to read. Further troubleshooting may require taking voltage readings. A meter may become necessary. It doesn’t have to be expensive tho.