I have successfully gotten everything to work out now! I did a fresh install of Retropie 4.1, and the bluetooth connection worked straight away after installing the drivers. Maybe it is possible that trying to update Retropie from an older version was making something corrupt? I had not updated for probably close to a year or so, if not more. Even though I now have to reload all of my roms and everything, it seems like a small price to pay to get everything running smoothly. :) Hope this helps somebody else too!

-Ibprofen98