I think I know where I went wrong, there are two nuts that go on studs for the valve cover and I think I needed to tighten them down before I tried to thread in the rest of the bolts. Got to the job at 12 today and just now got out of the shower.
Aluminum valve cover absolutely whooped my butt today. Took off the intake and valve cover to put a new gasket on and had a massive leak on the back passenger side. Took everything back apart, reseated the gasket and used rtv, three bolts would not grab. Rough day.