Thanks Michael - I got this working.
For those that might run into this problem, here is what you need to do:
checked off to be able to read the repo, make API calls, etc.
- In Jenkins - create a credential type of "username / password"
- Your username is your github username. The password is the token generated by github
- In the multi-branch config - you should now have a username/password choice in the "scan credentials" drop down. Select the credential from above and you are good to go. No more API limits! (Well - 5,000 / hour - which should be lots)