When I had tried out how well the Dotstar matrix boards and NeoPixel stick fit into the case, I had determined that I should make the shell a little higher to allow more clearance for the solder joints and to have overall a little more space for the electronics and battery.
I glued 3×1.5 mm ABS profiles on all sides of the bottom frame part with ultra-strong 2-component epoxy and let it dry overnight. The next day I added more profiles (slightly intended), also with 2-component adhesive. This second row acts like a guide for the main shell when placed onto the frame.
A few days after the glue was well dried, I carefully filed down the PCV segments on the top and bottom of the frame so that the main shell would sit flat on the modified frame. I also filed down the inside of the top PCV profile a bit so that the NeoPixel stick would fit in better.
LED stick fitting testSection titled LED stick fitting test
The glue layers still look a little messy/rough, but that will change later when I glue the frame and main shell together and fill all the holes and gaps. For now, the spacers were sufficient this way and I decided to move on to other things first. I wasn't ready to finally glue the frame and main shell together.