I think LEDWiz is 32 outputs, so that should work for you. It also has screw on terminals, which will make it easier for you. I liked the Molex 0.1 on the PAC LED, cause I could get a 4 port Molex connector for each RGB LED.
You will have to buy the hollow shafts seperate, they don't come with hollow shafts.
http://www.paradisearcadeshop.com/en/paradise-arcade-custom-parts/422-sanwa-jlf-stainless-steel-hollow-joystick-shaft.htmlShort shaft is standard length, long is if you want to bottom mount through wood.
With those buttons and balltops, all you really need to do is find an LED you want. It could be clear or blue, since you are using blue tint balltops and buttons. Blue may give it a better look.
Stick to a 5mm or smaller for the balltop, getting it in that hole is going to require sanding.
For those buttons, you could use one of paradise arcade's pele rings, even though they are RGB, you can just hook up the blue leg. This would require you to get straight up blue LEDs though.
http://www.paradisearcadeshop.com/en/108-button-ledsGetting your colors to match up will be a challenge, just buy a few 5mm blue LEDs til you get a brand that matches the pele ring.
As far as running it, LEDBlinky is nice cause it can only turn on the buttons a game uses.
I don't know about harnesses, I like doing my own wiring, cause I can get the terminations I want for each setup.