@gsimpson4 This may not be the case for you, but I noticed on the upgrade, my assigned roles for administrators and publishers did not move forward with the upgrade. I was/am using Active Directory and the GIS Tier.
To correct, I opened manager, went to the Security tab, and made sure my Active Directory (AD) connection still was valid. Then I went into roles and reapplied all the "administrator" and "publisher" settings to the AD groups. By default they all reset to "user".
Personally, although it's a slight inconvenience, I don't think this is a bad thing with the upgrade. At least it makes you revisit the security a bit.
BTW - I did have a smooth upgrade on my dev and prod server. I actually remove Desktop 10.1 before up upgrading server. I don't know that it was necessary, but I figured it would make things simpler. I then stopped the ArcGIS Server service. The install took a while, partially because we have a lot of services that neede to be restarted. (once complete, I installed Desktop 10.2)
For the Web Adaptor (on a separate IIS machine), I have two web adaptors installed...one with port :80, the other with port :443 (with ssl cert). The install recognized both ports. Only issue I had with this portion is when the "config" windows tried to come up for each of the web adaptors, it attempted to use "localhost" which on my IIS machine did not work. When I changed "localhost" to the DNS name, I was able to configure it for both :80 and :443.