Easiest is you setup the new bebot modules as you want, and simply copy over your old Bot.conf and MySQL.conf files. Then start using the new files.
Just remember that 0.5 loads all modules, even those with an added _, the actual loading is right now controlled by the modules conf.

If you want to make absolutely sure you can go back to 0.4.x you'll have to make a backup of your mysql database. Some 0.5 modules got updated table schemes, so they aren't backward compatible.

To use your new PHP version you can either put PHP into a dedicated directory and put it into the path to call it, or simply copy the files into the bot base directory and use them from there. The php files themself shouldn't have any influence on BeBot, as long as it's 5.2+.

If you aren't using it yet, read up the wiki page for multiple bot setupts.