I think you did fine.
You should be able to upgrade directly frm 4.6.3 to 5.2.3, but you might have ended up with some of the same problems.
In some cases, a problem with an upgrade script might have been fixed in a newer version.
Regarding upgrade from repository, you are correct. You can only upgrade minor versions from the repository without changing the repository URL. It looks like it pretty much worked.
Thanks for persevering. I think the upgrades are generally more reliable in newer versions, but it is not a well tested feature. It's very difficult to test it reliably without using real data.
