Default [Q] Bootloop with PA 4.0

I was following the direction in this thread

I downloaded pa_g2-4.0-ALPHA-20131205-ls980 for the rom and I am using pa_g2-4.0-ALPHA-20131205-ls980 as the GAPPS. I think I screwed up step 5 "5. RUN INITIAL SETUP & REBOOT." What does it mean by run initial setup? I just rebooted at this step which is most likely why I got in a boot loop.