I would switch to UniBeast/Clover and test it can boot your current Yosemite installation. Once you can boot it with UniBeast/Clover, then you can remove the kexts that have been installed to /S/L/E or L/E. The guide is relevant to UniBeast and macOS Sierra too. It was written when El Capitan was released, just replace EL Capitan with macOS Sierra.
Using UniBeast and MultiBeast will minimise any errors you might get if you installed Clover directly, since a good config.plist to start is mandatory, this is created with UniBeast and MultiBeast. Just the EFI Partition from UniBeast should allow your Yosemite partition to boot.