Any reason you have posted this twice?
Sorry to hear you’re having problems.
I’m having difficulty determining what exactly the problem you’re having.
What problem are you having with the stacks update? It’s working fine for most of us, but if you’re having a problem then it would be help if could give a bit more details on exactly what’s happening. Is it crashing?
I would doubt the upgrade had anything to do with putting out a PHP file as well as an html file. You didn’t say what version you upgraded from? If it was pre RW7 than the message didn’t exist. But more than likely a stack you’re using requires PHP and changed the extension automatically. RapidWeaver is a non destructive application and won’t delete files on the server. You’ll need to that manually, it’s not much different than deleting a file on your Mac.
As for the missing stacks after you upgraded, RW8 copied the addons folder to a new location. So the old folder is still on your hard drive. If you give the old version number of RapidWeaver someone can help you find them and copy them over.