Just fixed my problem. The issue was the flange on the header for #1 cylinder was just a bit too tall. The top of the flange hit the edge of the water thermostat housing and wouldn't seat to the head. Didn't want to grind the header and go through the ceramic coating. Took off the thermostat housing and ground a little bit off the bottom edge lip. That same flange also interfered with the intake manifold where I had to slightly enlarge the bolt hole on the top of the intake manifold to avoid cross threading the bolt into the head. Here's a shot with the area circled in faint red where I had to grind the bottom of the thermostat housing.

...been there, done that...

Dry fit, dam, grind, dry fit, repeat