Verify RGB Led Cube equipment
Capacitor ratings don't really matter in your case, as you are using only 5 volt. Only their values (F) do. 

Though the crystal you selected has an indication it needs 20pF load capacitors, not 22pF. 22pF is probably still fine. (Also note the ±20% accuracy, so between 17.6 and 26.4pF)

The IRF9531 and IRF9540N have the same pinout. They are also pretty similar in specs. The IRF9540N is slightly better even.

Note that the ATMega328p doesn't have the bootloader pre-installed. It's not that hard to do yourself though.

The EEPROM you selected is an SMD version. Kind of hard to work with if you are still a beginner. Better use a DIP version instead (that one is a bit more expensive, but 4 times the size)

I'd suggest you add an USB to Serials Adapter to the list, so you don't need the Arduino Uno every time you want to reprogram it, and use the Uno for something more useful.