Ok I have resolved this. I would like to thank you for your attempts to support, but as you point out the Self-hosting option is much more technical, and not something you support.
So, the solution for my problem was the following:
1. Snapshot the server,
2. Dump the db locally
3. Download the new files from the client area
4. Run the new files locally (localhost, on a local php server that is) with the old db and see what's going on, tons of suggestions and errors. First of all the engine needed to change to InnoDB to allow for a different way of indexing, plus tons of other db fixes and clean ups.
I did write a 10 page manual for our own usage until next time. No place for that here. Also, add the -TESTINSTALL flag when setting it up, but that's all in the manual:
5. Once done, it doesn't work with just uploading the files as they had been changed after the local upgrade
6. Go in to the server and manually delete all folders (except Images, Notes, Upload - your users will thank you) Do not delete via FileZilla etc. It will take forever. I went to the server and used "rm".
6. Upload "fresh" files that you did not use to upgrade your local, this is around 8000 files and will take 2-3 hours to upload.
7. After upload now you need to make a new Nginx configuration by "rebuilding the web app conf" (if you use Runcloud). Something needs to be refreshed and a server restart didn't help.
8. Now, once it's back again, you can run the /admin/ and login, and then use the upgrade feature which works surprisingly well, but takes a while, around 30-40 min.
9. Once done you are good to go. Snap shot again.
Bonus points for turning off your forum before doing all this (inside the admin panel), so they users doesnt try to write to your files while you are doing all this.
Expect down time of at least 5 hours when doing all this, not counting any mishaps or issues.
There you go!