Over the years I've searched for the PERC doco a few times and can't find it but there is useful info here
http://gamearchive.askey.org/Pinball/Manufacturers/Williams/pinbuilder/ which is where I first saw reference to PERC. It's not the same doco as shown in the Flash multiball video - does anyone have a link to it? Please post as it would be cool to see.
The Arduino addon is what I think would be a good way to modify games. Two ball multiball would always be easier - for example imagine Time Warp where you "lock" a ball in the collect bonus kick out then send another ball in towards that lock - either without hitting the standup at the top of the tunnel or by entering from the pop area side. How do you tell there are two balls stacked in the area without more switches or gates to prevent it happening?