I want to make myself a set of rudder pedals with toe brakes,
"Easy task" - if you are able (and have skill and tools) to make a good mechanic parts, the old "Baloo Pedals" are a good base to start, improve then with bearings, better center system.
Electronics today is cheap and accessibly, plenty of options, plenty of help in Internet. For example, can buy:
BU0836A controller - 36$.
DSD controller = 39.75$ (free worldwide shipping).
Or, get a Arduino PRO Micro/Teensy - ~20$ or Chinese clone for 5$, load MMjoy2 firmware. Topic about there.
All will be a PnP game controller using Windows HID drivers, no 3rd party drivers needed.
Potentiomters for USB controllers could be 1 to 100k - better use between 10 and 50k, the best compromise between noise generation and and electric consumption.
But, you need
30 to 60 degrees electric travel potentiometer, or will need use gears/pulleys or loose resolution.
Good luck looking for them in electronics stores.
BTW - Potentiometer wear with use and cause "noise" - spikes in axis response.
You can use good quality ones, that will cost more that the next option:
DIY HALL sensor - tricky to "tune" the center position. But easy with assembled like pot' ones:
http://www.digikey.com/product-search/en?mpart=6127V1A60L.5&vendor=987Or "Magnetic Resistence" sensor, like the Troll mentioned TLE5010/11 - they need a small PCB.
This kind of sensor are standard in the "Next Gen" pedals now available: Baur, MFG, SLaw, VKB.
3) I understand that having wired it all up I then need to program it. This is perhaps the most confusing aspect for me. Is there where some study of MMJoy's program is required? Is there not a prewritten code for 1 rudder pot and 2 brake pots out there that I can scavenge?
You don't need "program it" - the programming is done by Mega_MOZG, nor deal with sketch codes. This is need for "Arduino Start Kits" like in your link, what is for the guys that want learn programming Arduino's, you dont need this.
What you need do is
load the MMJoy2 firmware in Arduino PRO micro, what is like record a file in a DVD in Windows, or upgrade Warthog, or VKB Mamba, Gladiator firmware.
Don't require extra hardware, use the connection of USB cable.
The advantage of MMjoy2 firmware is their flexibility, you can set the device name, VID/PID, number of axis, axis names, axis resolution, filter, axis curves and more.
If you find a "prewritten" code will be limited to what their author think is good.
If you want add CAM center in your pedal PM me I "translated" a Russian document about the basics. "Joystick CAM for Dummies".