Intake manifold/cylinder head rocker cover missalignment
 

Just finished installing Victor Intake and Edelbrock heads on FE. Although all the bolt holes in manifold and ports lined up very well, I have about 1/16" or less missalignment between rocker cover gasket surface on manifold and heads. Is this typical? Having worked on small blocks for many years, never experienced this.

That amount of misalignment is pretty typical. Because the 2 surfaces are not machined as a unit there is always some. When I was a machinist, I machined several of my own so they were flush. It took a lot of labor that most wouldn't have paid for at the time...probably still not. Of course the problem then arises when another intake or head(s) are swapped, it was only machine for the ones. Modern sealers and trimming of the intake gasket tops usually seal fine. Unless you are already torqued down you might fit it without the manifold end seals, that will sometimes allow it to set down further, just use sealer on the ends......allow it to cure well before torqueing.

You're lucky that's all that is off.My RPM had the passenger bolt holes off to the front,the drivers side were off to the rear and the rocker cover bolt holes were splayed.
EDELBROCK QC SUCKS.

Misaligned holes
 

The holes in mine were off too. I couldn't even bolt the valve covers on. Sent it back to Jegs and got a new one which was fine.

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Have you checked the alignment of the whole package. I fight pretty hard on some of these - and really hard on the rest of them :)

Stick some intake gaskets on the head - I use Fel-Pro MS90145 for this because they have nominal embossments and are "hard" material.

Use the distributor as an alignment "peg".

Square/level the end seal areas (aka china walls) front and rear.

Take a feeler guage and stab the gasket face top and bottom on all four corners - you'll get an idea whether the intake is square to the heads or not. I mark my measurements on the intake with a sharpie for reference.

Now look into the ports to see how the ports line up to the heads. If the intake is too low you need thicker - or doubled up gakets. If it's too high you need to note the amount of misalignment because you'll need to mill that amount off that flange no matter what.

Now you take your required flange cuts and make them on the angle that reduces or eliminates any of the angle issues you identified.

Test install again and - if you are lucky - all the ports now line up, the distributor is centered, the flanges are square to the heads. Test install bolts and make sure that they go in smoothly and don't hit the intake on an angle (they will crack the boss if they do).

...ohhh - and on a Victor you really need to check the sharp corner they leave at the inner bottom of the port flange - it often hits the head gasket....

Thanks for all the input. I did check for squareness at the four corners and it was very good. I'm trying to contact the guy who machined my block. He said he was going to take .005 off the decks for cleanup. I've been told that .005 should not make a difference. Maybe he took more off than he told me. Since I will run the engine on my own stand before it goes in my Cobra,
for now I might leave it as is and correct later if a problem.