I question exactly how my boss (Director of IT) got his position since just yesterday I was having to explain to him why 8GB of RAM on an x86 is a waste of money.

Managers are not hired to necessarily be technically adept. They are hired to manage people. We hire technically adept people like you to do the work.

Even after that, the update process took an additional 8 hours. He's all for an imaging system but is that even a priority right now?

You answered your own question in your explanation. You wasted 8 hours doing updates that you could have done something else and those computers have been off your desk and in the hands of the customer.

We are deploying electronic medical record type software right now by taking our trusty thumb drives and physically going to each location for install rather than rolling it out automatically using GPO or SCCM.

This is cost to creation thing. Does it take more time to build and test a package to deploy to 10 people in the same vicinity than it takes to just touch each of those 10 computers and do the installs? Could also be a lack of talent to create those packages efficiently or difficulties with the way the software configures to have it deploy effectively via GPO / SCCM.

I don't even know where to start here...What did I sign up for?

Work. This is what you signed up. Part of this may be new guy hazing to make you do it the hard way to better appreciate the easier way. Part of this may be old school thinking by management in how things are done.

The most important thing to remember is that you will not fix all the problems overnight. Do not take every battle to heart, but do everything in your power to work smart and do quality work. If they do things a stupid way, don't hesitate to ask why and propose a better solution but if the ultimate answer is "This is how I want it done." then you just button it up and go do it. It isn't worth the fatigue to fight the battle.