Actually I had sent Neal (who sent Lumintop) the updated board files to have the swapped miso and mosi lines a long time ago, so we're not sure why Lumintop went with the older board files for fabrication. In any case, I don't have confirmation yet that future batches will swap the MI and MO programming pads, but I have certainly raised it up to Neal again. Apologies for the trouble but I did my best to convey the message to use the latest files for production, and I can confirm that Neal has received updated files.
contactcr is right - the easiest way is to simply get a bunch of female-female 0.1" headers and make your own cable, if you're using the Emisar pogo-pin flashing kit. These headers are cheap and plentiful. You can also use female-male headers if you unplug only one of the sides. This set on Amazon is fairly cheap and has all 3 variants: https://www.amazon.com/Elegoo-EL-CP-004-Multicolored-Breadboard-arduino/dp/B01EV70C78/.
If you're planning to modify the firmware, please get the latest version specifically for the LUME1-FW3X from either TK's repository, or the github page with the latest Anduril firmware.
There are some modifications that were made to Anduril to help take advantage of the additional hardware in the Lume1 driver, so it's a little more advanced than other Anduril-based flashlights. Some of the base files (non hwdef or cfg files) are modified specifically for Lume1. One example is the external temperature sensor handler. The comments in the code should describe these in detail.
For soldering the Aux LED boards, Scallywag has the right idea. Use some flux and just a touch of solder. I highly recommend using tweezers to hold the wires and pre-cut and tin them to length (details in the datasheet PDF here: https://github.com/loneoceans/lume1-fw3x-anduril/). Solid core AWG30 is great, but any other thin wire of your choice will work well too. There are also detailed instructions about prepping the flashlight for driver replacement.
Just a suggestion: this 8-stranded multi-colour wire-wrapping wire works really well, but the insulation is prone to melting at low temperature, so it needs a little finesse when soldering to prevent the tweezers squeezing the (melting) insulation: https://www.amazon.com/URBEST-Solder-Coated-Wire-Wrapping-Celsius/dp/B01LWI20M0/. This wire is also great for PCB rework since it's solid core.
For the FW1A, I actually do not have one myself so I cannot test nor verify that it will work, but there should be no reason why it shouldn't work electrically, as long as it fits mechanically. Just be careful with the turbo-mode; direct drive FET may be too much for a single XPL LED, so you may have to limit it by perhaps using some 'low-drain' cells like the Panasonic 18650B, and make sure that the heat-sinking of the LED is done really well. However, there should be no problems with FET drive if a 3V XHP50 is used.