Agrajag, good to see you've taken the plunge.
The Ipac56 (which has the choice of usb) is a good idea just in case you decide on making something bigger in the future however having some buttons shared is not an issue as you could share each of the pinball buttons with any of the other buttons. But as you are having 24 (25) buttons and 2 joysticks (4 inputs each) giving you around 32 or 33 inputs - go for the bigger encoder if your budget is able to.
For the layout I have gone for
http://home.iprimus.com.au/craigrb/images/New%20button%20layout.jpg which is very comfortable. Will have the players credit and start buttons somewhere else (haven't decided yet).
I have Happs supers, Happs opticals and T-stiks (from ultimarc) which are all bat style handles and you can see them on my site. Only get opticals if you want and like to play the games that need the optical joystick. They are very expensive. The supers are very hard to change between 4 and 8 way as you need to get to the bottom of the shaft, remove a clip, turn over the hourglass piece and put it all back together. The t-stiks have a switch on the side which will still require you to go into the panel. They are also shorter and don't have much movement.
Like Nailz said go for oscar spinners - great product and he is very helpful. He also has restrictor plates that can make the joystick into 4 way or 2 way without going into the panel which is what you are looking for.
There is eventually going to be a usb release of the optipac which you can plug the happs optical (if you get one), spinners, trackball. Are you going to go for 2 spinners and 2 trackballs? 2 spinners will require you to use +analog for axis splitting. Also if you get 2 usb trackballs you can also use +analog (I think). But if it's just one of each then it would work fine. Some people hack the trackballs into usb mice if not usb already and I think there are some tutorials on it around.
So the Ipac would require 1 usb port and depending if you are going through the optipac (which isn't usb yet) that would be another. Otherwise you will need a usb port of the spinner and one for the trackball unless you swap them out when you want to use them.
Other electrics - wires, quick connects, PC, tv/monitor, power, marquee light, power tools (yeah) but get all this from local shops.
Hope this helps and good luck with the planning. Post pics, links on how you proceed and any other q's you might have.
Cheers
-cdbrown