Glad we figured that one out!
Yes I would try jupgrade again. When you set the parameters for Jupgrade you can choose to rename the folder, so you can put the upgrade into a new one and not need to delete anything. Of course you'll use up some diskspace, but you'll have several test sites. So deleting it is optional.
Keep a backup. I always backup the entire site, and a separate database backup. That way I can always rebuild a site if i have to. Be sure you run install, update, database and warnings on the jupgrade version and all is working perfectly there.
You should be able to copy the files from the Jupgrade folder instead of move them so we can go back to them if we have to. Don't delete them until you have the main site working.
Probably this was the problem with the first attempt as well. If you move it and cant' access it, what we just did this is the same fix I would have tried for that.
Ed