Did your leaky gasket only have two layers?

The gasket has 3 layers - I just separated 2 of them with my fingers while trying to hold it and take the photo!  The only noticeable difference was the lack of the black coating on the backside of the top and bottom layer.

Now that I've rambled on about two-layer vs three-layer, I have to add that I always had oil permeating all through the OEM gaskets on teardown.  There really isn't much of anything to keep the pressurized oil from migrating throughout the layers.  The rolled beads face up on the top layer and down on the bottom layer, so I have never figured out exactly what is supposed to keep oil from squeezing through the center of the sandwich.  I switched to an external oil feed to eliminate that gremlin.  The increased oil pressure from the high-speed gear drive only aggravates the condition.

I am going to use an OEM Suzuki gasket, and I have been considering the application of a very small amount of the Permatex Motoseal around the hole where the oil supply comes up through the cylinder and goes into the head.  I have been thinking that is needs to be a very tiny amount of sealant - just a thin smear.....as it will have to be applied twice to coat the interface between the 3 gasket layers....and then again twice more for the top and bottom of the cylinder head.  I don't want to make the gasket too thick in this area and prevent the cylinder head from being able to properly seat on the cylinder.  Motoseal is very liquid and can be applied very thin, and it spreads out easily once pressure is applied.  

I see a nice ring around the forward head stud hole in the cylinder.  I am guessing your stud is staying put and hasn't started migrating downward.  Looks like the shiny condition is due to zero coating transfer from the gasket to the cylinder deck, a clear sign that the shoulder on the stud is not bearing against the gasket (a good thing).
How does the stud look?  Is it proud or recessed?

This exhaust stud looked fine and is recessed as it should be.  I have never experienced the exhaust stud pulling the way that you did, and I believe I assembled this engine before I saw your post on the modification to the stud.   However - I am currently in the process of using the plumbing tool to cut the recess for the fitting inside the exhaust port...and I machined the inserts a few weeks ago.