Who cares? Even the stock SOHC paper gasket doesn't line up perfectly. That and when it comes to coolant passages, you don't actually want high flow at all locations.
All that matters is that nothing is going to leak and all the passages needed are going to work. BTW, OEM MLS vs aftermarket MLS....they are not proven similar.
I already posted that I used DOHC cometic 95mm headgaskets (and that large bore is not needed). You don't need custom headgaskets. This has all been posted before in this very thread, I don't see a need to rehash it once again. Go back and read what happened already.
Here is an option which I cannot endorse but it exists.
http://www.3sx.com/store/comersus_vi...?idProduct=779
"All gaskets are the stock .051" thickness." Which again means you don't have an OEM turbo headgasket so you keep skirting the real issue and real advice here. I will note that those are not OEM headgaskets either.
I don't remember your bore size, the thickness of all the headgaskets you have tried. I don't know why anyone would mill much of anything off a 6g72 deck.
The big hp builds often put a small taper on the top of the piston and then use a stock OEM MLS turbo gasket.