OK. I've started over, again.
This time I used my Yosemite installer from my macbook air (instead of the yosemite installer from my mac mini) to build my USB installer. I have reinstalled yosemite. I ran the pbi beta 6 and updated clover installer from inside clover config. Clover bootloader runs, I choose yosemite, and the screen just goes black. I have no way to get back into OSX. My EFI was completely empty, so any files loaded there now would be added by PBI. I have no idea what else to do but wipe the drive and start from absolute zero, but I don't think that's going to fix it.
OSX loads fine before I run pbi. I am going to post my NEW clover files from my most recent installation. Here's the full EFI folder. The only thing I added was the microsoft folder so I could boot windows and type this. everything else was pbi.