Bought an in/lb torque wrench and a timing light. Retorqued the intake manifold to 11 ft/lb or 132 in/lb, and glad I did, it was loose. Torqued the valve covers to 20 in/lb. That was a guess but is also the lowest setting on the torque wrench. That took 4 times on each side to get them even, the intake took 3 passes. Then timed it and routed some spark plug wires and vacuum & egr lines better, since my friend that helped me swap in the vortec heads last November didn't route things very well.
Took it for a test drive and I am thinking my suspected rear main seal failure was just the loose intake and valve covers. No fresh oil smell, no drips, and it ran nice and smooth and very strong.