Hello @Greg Bemis !
Welcome to Microsoft QnA!
For the license question Azure Ad Free is enough and you can have a detailed look here
Also check here because MFA is now a must and you might consider Azure Premium P1 as an add-on
You don't have a problem with the domain names . Actually this is a common thing so the only thing you have to do is add a UPN Suffix and the users will be synced just fine
The mechanism of Azure AD Connect is quite advanced with a lot of options and features. Among them is the Sync Rules Editor
You can also apply OU filtering along with Device Write back and Group Write back
I would suggest considering Azure AD Premium P1 , for the Identity Security Mechanisms and the MFA Controls
I hope this helps!
Kindly mark the answer as Accepted and Up-vote in case it helped!