I would suggest adding back the TestMode to the list of plugins, as that is one of the easier ways to figure out if something’s wrong. To do that, add #include "Kaleidoscope-Model01-TestMode.h" to the top of your sketch, and &TestMode as the first (or at most second, after &BootGreetingEffect) entry in the Kaleidoscope.use list in your setup() method.
Flashing a firmware with this, you can enter the test mode by holding Prog + LED and the left Fn key. Then, you will have to press a key (any key, and you can press different keys each time) four times (if I’m counting right) to enter the matrix test stage. Here, press each and every key exactly once, and note down what color they light up with. If you can post a photo of the keyboard at the end of this, that would be great, and we can proceed from there.
You can also email help@keyboard.io, which is what Jesse’s been suggesting to people who saw similar problems.