Not wanting a repeat of previous mayor upgrade events I decided to wait a little before I attempted to upgrade my VSA. I also convinced my boss to allow me to spend some time performing a test upgrade first. I restored our VSA, SQL server and a Domain controller in our test lab and attempted an upgrade on the VSA.
The licensing got me first but luckily after wasting some time with Kaseya support over the phone, Michael Dixon (TY) gave me a SQL script to purge the agents out of the VSA and I now had a fully working duplicate of my production VSA environment. Something I would like to see Kaseya do here is make it easier on us to purge agents out of the database and not block you from doing it via the VSA portal.
I was very impressed with the installer, it found some IIS issue that it even fixed for me, Kaseya must have spent a fair chunk of time on it, Good Job! 
Despite the impressive installer and around 1GB of setup files, the post install hotfixes let it down with one of them failing with non-specific error that took me to Microsoft IIS page that did not match the error in question. I continued the hotfix process by rerunning the VSA hotfix URL and the install completed.
The next problem I ran into is logging on to the VSA with my domain account, I had to bypass this with my backdoor account. I found out the reason why my domain account was no longer working was because of the new Discovery module. I tried to get it to sync the domain accounts via the "Domain Watch" but it is stuck on preview and has been stuck on this since yesterday morning.
I thought one of the possible reasons why the "Domain Watch" was not working could be caused by the older agent version on my domain controller so I attempted to upgrade agents. That did not work either and I had to manually install the agent on the domain controller the second agent I tried to upgrade is still scheduled to be upgraded and the upgraded agent on the domain controller made no difference to the "Domain Watch" issue.
Another big issue I found is that all of my Policies under "Policy Management" are missing this was a lot of work and would be a big upgrade show stopper for me at this point.
Anyway I have logged a ticket before I started the upgrade and I updated it this morning with all of the issues I found post upgrade.