First, stop running PowerShell commands on SBS! The commands do their job, don't get me wrong, but the wizards also set some registry keys that the commands (not designed for SBS) do not do.
In SBS, always use the wizards.
So, with that said, a couple of things:
1) Outlook attempts autodiscover.* by default. This is hard-coded, cannot be changed. The solution here is to make sure there is no DNS entry, either directly or by wildcard, that will answer that request. As long as there isn't, Outlook moves on to the next attempt. This is normal behavior and will not cause a problem if everything else is set up properly.
2) Run the Fix My Network Wizard followed by the Internet Address Management Wizard to reset your domains in all of the appropriate places that the powershell commands have only half completed.
3) Rerun the certificate wizard to reassign your public GoDaddy cert back to IIS and Exchange (the IAMW will create a new self-signed cert.)
4) IF you are still having certificate issues, post back here so we can help resolve them the right way instead of resoritng to PowerShell.