Well I think it can be better. For example, upgrade instruction state specifically to choose the next version up to upgrade from, if you don't see the version that you have available. Because I had 4.0.1 and there was either 4.0 or 5.x, I selected the latter one. Then I was to find out that I should have selected 4.0. It is little things like this that can cause confusion.
And yes ideally the file permission part should have been copied over. But how about a FAQ section on upgrade issue as part of the upgrade manual? Some programs have this available and it helps.
In any event, just a suggestion.