I had some time last night, so I checked the new manifold vs the heads.
Valve Cover Rail (intake): 0.095" high
Pushrod Holes: Concentric, looked fine
Bolt holes: Concentric, bolts fit nicely
Port Depth: Within 0.020" based on scale measurement
China Wall clearance: Same as previous, worked fine
Basically, it looks like everything lines up nicely except for the valve cover rail. If I get this machined so the rail matches by machining the intake face, it'll negatively affect the other areas that are currently aligned.
Does anyone have any CAD (2D or 3D) of a head, gasket face, or intake side? I am thinking about manufacturing a steel shim that matches the profile of the valve cover face on the head and appending it there to make up the difference. That, or if anyone sells a 3/32" thick valve cover gasket, it would fill that gap perfectly. Any other ideas? It looks like the previous owner had it sealed up fine with the same gap on the stock iron intake by being generous with silicone on a cork gasket.
I don't have the budget this year to pull/replace or machine the heads unless my motorcycle sells.