Thank you for reporting this issue. The problem was that I forgot to change the plist files for the SingleLink Alternate framebuffers in the 10.9.5 QE/CI package. I have reuploaded the package so it should now be working.
For those users who are wondering about the QE/CI package for OS X Yosemite Beta 3, Apple did not update the Intel HD Graphics kexts. So if you want QE/CI (full graphics acceleration) on OS X Yosemite Beta 3, just install the kexts from the QE/CI 10.10 B2 package.
Try the new uploaded QE/CI package for 10.9.5. Maybe it works now. Again, use the SingleLink Alternate LW1 framebuffer.
I downloaded the newly uploaded 10.9.5 kext file and still freezes up at boot with the spinning wheel. I just can't figure out for the life of me why it works perfectly for 10.9 with the appropriate kext file, but this one doesn't want to work no matter what combination I try with the kext file. Thank you for all of your hard work! It really is appreciated