Short version: the solution for me - remove iTunes and reinstall 12.5.5.5.
Long version (more to share my pain then anything else) - the link with all previous iTunes versions (Troubleshooting issues with iTunes for Windows updates):
It's my own fault, over the last couple of years iTunes has upgraded with no issues and I became complacent with my backups of my iTunes library that has music i have owned going back 35 years.
I clicked on the yes to upgrade iTunes without thinking about it. That was Sunday, today is Wednesday and finally my library is back intact.
Finding this thread earlier would have saved me a couple of days troubleshooting but I have learned a lot more about where iTunes stores its information and have since backed all locations up.
I am running Windows 7 on the media computer and Windows 10 on all laptops.
The upgrade to 12.6.0.100 appeared to complete without issues, however, when it hung on loading for a good 4-5 minutes. The usual reboot, killing iTunes and restarting did not resolve the issue. After i waited long enough my media appeared o.k. however the store would not load, and syncing an iPad hung at transferring purchases and I had real trouble backing it up so i could not upgrade to the newest iOS.
Followed all the usual troubleshooting steps, reset the network stack and rebooted, uninstalled iTunes, reinstalled, uninstalled and removed all remaining directories and rebooted, reinstalled - so much time waiting for uninstalls and reinstalls, hoping it would work.
Installed 12.6.0.100 on my Windows 10 laptop - no issues connecting to my library (which is on a NAS) and the store.
Both are on the same network, behind the same firewall, yet Windows 10 works and 7 does not.
On Windows 7 I started watching the resource monitor and sorted by CPU status - iTunes was not responding, right click and analyse kill chain showed to TCP processes that were waiting to complete. This looks like a network problem to me.
Installed Wireshark on both, captured the startup and also ran the diagnostic from both installs - just the network connectivity tests. The connectivity test on Windows 7 showed that iTunes could not establish a secure connection. After going down more rabbit holes Wireshark shed some more light on the issue.
Windows 7 running 12.6 does NOT perform a DNS lookup for Apple related services (though it does for Gracenote) - the program itself is not performing the very first step required to connect and get the IP address as it is not even trying.
Complete uninstall and found this link (Apple - Support - Downloads) to download a previous version 12.4.3 for older video cards. This worked, however my iTunes library was now completely destroyed. I had a full backup from 14 months ago on an offline NAS which I got out of the cupboard and powered on. For my library the only recovery option was to import the iTunes library XML file, thank goodness I had enabled the "Share iTunes library XML with other applications" before I backed up. This took at least 8 hours and I then used a paid version of TreeSize to compare and copy the media from the backup to the iTunes media library as during this whole process at least 10GB of media had been removed by iTunes (thank you Apple). I then rebuilt the library by enabling "Keep iTunes media folder organised" and "Copy files to the iTunes Media folder when adding to library". Goodbye another 8 hours.
Next was to redownload all the songs in the cloud and cover art, import the folder containing apps and tones (as both were showing as empty). Last step was to backup the entire iTunes directory to a new folder on the NAS.
Thinking this was it, I connected my iPhone to sync and it wouldn't as I must have been on a 12.5 version of iTunes.
As I now had a full backup today I decided to upgrade again back to 12.6.0.100 (still broken on Windows 7), I then installed 12.6.0.95 (also broken, and yes you have to fully uninstall the newer version and reboot before you can install an older version).
An entire list of all iTunes versions are available on the official Apple site here (Troubleshooting issues with iTunes for Windows updates).
An lastly I installed 12.5.5.5 which works and shortly afterwards found this thread - yay.
So the moral of this story is to have a decent backup of your iTunes library and dont be afraid to click no to upgrading iTunes.