My friend, if I could just follow the guide I wouldn't have needed to start a thread asking for help. I've read through the guide a couple of times. The guts of it, the software side, is fairly opaque to me.

The guide is fairly clear on what to do to setup a new file with no existing documentation, but I don't trust any of my measuring devices to get me close enough to a good measurement.

Well you have to be a bit more specific than "it's opaque". What specifically do you not understand. We have tens of thousands of users and nobody has ever said "I don't understand a single thing in there" :)

If you find the guide clear on how to setup a new file, you should find it even easier to setup if you already know the values from your Marlin config …

It's really straightforward to move from Marlin, and what I mean with this is : if you have configured Marlin, it means you understand Marlin's configuration options. If you understand Marlin's configuration options, then you understand Smoothie's configuration options, because they essentially do the same things.
So if you understand Marlin, you understand Smoothie, and you mostly shouldn't even need the guide.
Not only that, but Smoothie is actually easier than Marlin to configure, so that should help further.

For example in Marlin to set steps per millimeters, you set : 

#define DEFAULT_AXIS_STEPS_PER_UNIT   { 80, 80, 4000, 500 }

And in Smoothie, you do :

# Arm solution configuration : Cartesian robot. Translates mm positions into stepper positions
# See http://smoothieware.org/stepper-motors
alpha_steps_per_mm                           80               # Steps per mm for alpha ( X ) stepper
beta_steps_per_mm                            80               # Steps per mm for beta ( Y ) stepper
gamma_steps_per_mm                           4000             # Steps per mm for gamma ( Z ) stepper

As you see, you are setting the same things, it's just a bit of a different format.

If there is any specific thing you do not understand or need help with, don't hesitate to ask.

I didn't configure Marlin, though. I got a good printer with a bad board, and the existing files. I've helped a friend that is even less technologically advanced than I am to ensure his Marlin code compiled properly (bad values, a couple of incorrect references, a couple of basic fixes like that) and went in and changed basic settings on his such as overall height of the printer and a couple other minor things, but beyond that I haven't gone through from A to Z and configured a file.

I've never configured a file from scratch. I know that I have the correct settings in one file, and I should just need to move those files over but I don't know what and where.

Ok that's not a common case, vast majority of marlin users actually configure it themselves, and therefore understand the options, so when they come to Smoothie, they understand what Smoothie's option mean because they are the same.

I think you need to read Marlin's documentation to understand the Marlin file you have better, and once that is done, you need to go over the Smoothie guide, do what it does, and take it one thing at a time. If you run into trouble, just ask for help here.