To my knowledge the factory steel shim is .019-.021. Call it .020..lol splitting hairs right...
So you milled .100 and added .046
So the head is sitting roughly .054 lower than it was.
One way you could have a vac or oil leak is if the The Machinist didn't set the head up right on The Jig when Milling it. A lot of guys don't do the old scratch test. You mount your head up on the jig... you get your levels out n you check it make sure it's level catty-corner across and long ways...then crank it down TIGHT and check it again...then you dial the cutter head up to clear the deck by a visual amount and move it over the end of the deck surface of the head...then uou then spin the cutter by hand and slowly dial the cutter down till it just scratches the head...now with it hand spinning still... you move the cutter across the deck while watching the scratch width..it wants to be even...wrong look a like narrow to wide as it goes across... this makes damn sure you are making a level cut and not deviating from the factory angle. I always do that, checking your level accuracy and beyond any margin of error.
Not all machines are the same, some do it digitally. I started with the machinist 1st because you stated you had him mill .100
With that said, it could only leak if A.. he deviated on the cut..so the angles are off. B... The intake is tapered or ootb incorrect angle-Common on those.
Or C... you used the metal gaskets on the aluminum ld340 and that's a leaker every time. Been there done that and bought the t shirt. It's almost a prerequisite. Lol
Like mentioned, look close with light under it or behind it to see if the angles are off.
Also keep in mind many use thick gaskets..and the gasket can eat .025 worth of gap on the bottom..so they never know.
Pics?
