Thats a pretty good collection. What they need for flexible connections or other offboard connections is male terminated wires in housings that pololu.com sells. Can make up whatever size you want, from single wire to 2-3-5-6-8-10, etc. and they plug right into the female headers just as if you’d soldered 0.025" square pins on the end of wires to stick in the female headers.
Of femae terminated wires in housings to go onto male pins.
I have an enclsosure with a pro-mini with 2 female 6-pin headers and 2 custom LED boards with 10 pin female headers. I have 2 cables with 10-pin male housing that breaks out into 6 pins to plug into the pro-mini and 4 that go to a dusub connector for power/ground and 2 signals. Soldering the headers went quick, then popping all the terminated wires into housings and popping them onto the boards went fast. Sure, could have gone board-to-board (and did for the first pair of enclosures), but we were making a half dozen and this way one person could solder the headers on the boards while a second made cables, the result is something more modular and I didn’t have to try and clean flux off a bundle of 3 boards all connected together.
I have another project where I use 2, 5, 8, and 10 pin cables & headers to connect 6 different wirewrap boards together for different LED display panels to one control board.