My end game is to get as many inputs as possable out of the unit. I will probably need to find a way to link them so that I will get about 100 in and 100 outputs.
A 100 inputs to a single A/D line is possible if the ambient temperature and relative humidity doesn't change by any noticeable amount and if you can keep noise completely away... IOW you'll probably have to settle for less.
The method is simple though, just make a resistive divider with one common resistor going to a stable reference voltage and let the switches connect a resistor to ground.
If you need to be be able to push more than one switch at a time, you'll need to either use "binary" values (like 1, 2, 4, 8, 16...etc) or values for an R2R ladder.
Either way, you need very precise (i.e. expensive) resistors and it will be much more expensive than just buying a microcontroller with eg. 100 pins and use that for expansion (a microcontroller is a few dollars - high precision resistors bought from a high street shop may come at a few dollars a piece
A 100 outputs... Forget it, plain and simple.
What on earth do you need all that I/O for anyway?