Hi Pfinnegan,
Thanks for using Apple Support Communities to post your question. If you are having issues with using email clients with your Apple ID after setting up two factor authentication, you will need to download the iCloud for Windows v5 and the latest version of iTunes. This will allow you to use your trusted device to authenticate your windows PC. Please have a look at the link below for more details.
Two-factor authentication for Apple ID
With two-factor authentication, your account can only be accessed on devices you trust, like your iPhone, iPad, or Mac. When you want to sign in to a new device for the first time, you'll need to provide two pieces of information—your password and the six-digit verification code that's automatically displayed on your trusted devices. By entering the code, you're verifying that you trust the new device. For example, if you have an iPhone and are signing into your account for the first time on a newly purchased Mac, you'll be prompted to enter your password and the verification code that's automatically displayed on your iPhone.
What are the system requirements for two-factor authentication?
For the best experience, you should make sure you meet the system requirements below on all the devices you use with your Apple ID:
iPhone, iPad, or iPod touch with iOS 9
Mac with OS X El Capitan and iTunes 12.3
Apple Watch with watchOS 2
Windows PC with iCloud for Windows v5 and iTunes 12.3.3
This information will allow you to get
your Mail, Contacts and Calendars set up asap. Have a great day.