Windows screwed up my bootloader, and then I made it worse.

Had a perfect working Capitan install using legacy clover efi. I needed to put windows back on the other side for work. Overwrote the bootloader, I used the bootable USB I installed from to get back in, and I promptly downloaded and installed the newest version of clover.. which I guess wasn't what I was using before.

I can only assume I didn't have the some config.plist settings as before, because it won't boot from clover now, have to use the usb. I tried import the plist from the usb and copying to the EFI partition but that made it crash on boot.

I'm guessing the best course of action is a fresh install?

Unless there is something I'm overlooking

Thanks