I've begun opening up the side ports to 7/8 inch with a dremel sanding drum to accommodate the neopixel holders but it's a slow process because the metal heats up so quickly and I want to get them perfect. More on that later.

In the meantime, between sanding to ports, I'm assembling and testing the double battery - 3 position switch set up.

I'm using a 3 position SPDT switch (On-Off-On) as both a kill switch (Off) and to toggle between the two 21700 batteries. The white wires will attach to the center pole and connect to the board (-) and GND. I wired up three separate for easier connection to the board.
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Next I pulled the two JST connectors for the batteries into the chassis, the negatives from both will connect to the two outer poles on the switch, this will toggle from one to the other so only one is running at any given time (refer to 1st post for wiring diagram).
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I'm leaving slack in the JST connectors, need to determine if they'll be tucked into the bottom of the chassis or kept in the reveal cavity under the battery so having a little slack gives me options once all the wiring is in place.
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I added some additional electrical tape in addition to the heat wrap on the solder posts since the switch will be very close to the board when all is installed.
I won't glue the switch into the chassis until everything is wired up and tested, for now it's just loose.
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Next up, I'm testing the switch and connections BEFORE wiring up the board, just to be safe. These are new batteries and I haven't fully charged yet so the voltage is low, but I'm only testing the switch works as expected to cut power and toggle between. I have the battery positives connected to each other and I'm leaving the three board (-) from the center pole of the switch separate and testing individually to confirm everything will run as expected. This also cuts out a variable later should any wiring issues pop up. I'm confirming the batteries and switch all run and the electricity can flow to the board for all three points.

When the switch is in the center (OFF) there is no power.
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Next the switch is turned to the Left "ON" position and we have power - I tested each of the three white board (-) wires individually.
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And the switch in the Right ON position, also tested each white wire individually.
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Now that that's all wired up and working I'll keep working on those side ports. The top portion for the emitters is getting the most modifications, so I knew going in it would be the most time consuming, but once it's all done things will be downhill from there on out. I'll probably start building the blades next and work on the side ports and other mods to the top section as I go.

Slow and steady but coming along...