The best way to update is to rename the old .mupen64plus to something like .mupen64plus_old and then follow the first post's guide again but this time using the newest version from javispedro. Then just configure it like in this post and transfer your savefiles from the old foldier. The new version is much faster than the older one, for example Super Mario 64 runs nearly fullspeed (just some slowdowns here and there) with no OC. Only problem is that it doesn't seem to support transparent parts in sprites (nothing big but still).