Well Leonardo Pro Micro has a great price but it does not have enough ports pulled out. From 26 useful IO pins of ATmega32u4 only 18 pins pulled out to the PCB edges. But almost for sure you could hack it to get the additional 2 or 4 pins out too. For comparison, Arduino Micro has 24 pins easily available, and Teensy 2.0 has 25 easily available pins.
The other option is to make the matrices like this: 4+3 (keyboard) + 4+3*3 (led matrix) = 20 pins, but you can share the 4 keyboard scanning pins with the 4 pins of led matrix, so the needed number of pins is only 20-4 = 16 (which your Leonardo Pro Micro can easily provide).
The RGB LEDs you have look OK. Since they are common anode you would need to use FET-P instead of FET-N, flip polarity and flip logic in firmware. It does not really matter if your leds are common catode or anode ... you just flip all logic and that is it.
I cannot design and build this with you since I'm used to KICAD (and lazy to learn Eagle), and (much more important) I already have a project on my shoulders:
katy keyboard. Maybe you can find somebody else.