I only chmod the permissions listed in the install guide. I uploaded only the flies/directories listed in the upgrade guide. When I first started to upgrade, I did upload all the files except for the 3 you listed. But the install script wouldn't run. So I replaced my server ubbthreads directory with one I saved right before I started. Then I copied only the files listed in the upgrade guide and the upgrade script worked.
I am not sure what a CDN is.
I will clear my browser cache and see if I get a different control panel style to display.
I will change the permissions to 777 and 666 when I get some time. But if that is what is needed, why doesn't the install guide reflect that?