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You can install Xoops-Protector for added security.....
As for upgrading, since you have so many steps....
Easier I find is to reinstall it completely...
Take the information of each modules MySql, separately first...
Then install the latest version of Xoops....
Re-install each of the modules....
Then overwrite the information for each module.....
Then you get a clean copy and don't have to upload then upgrade, upload, upgrade, ect....also finding all upgrade scripts...
Just an idea, else you can do all the upgrades individually otherwise....which should be ok as long as you do each as instructed, as most peoples sites have had to be upgrade like that.