It’s doubtful you have two different intakes that won’t seal.
Make damn sure the manifold isn’t sitting on the china walls.
I’m not sure why .028 gaskets. That’s pretty thin and usually has limited use. I used thin gaskets like that when I needed a thinker gasket and couldn’t get one. That’s basically a .030 gasket and I’d stick that with a .045 or .060 to get **** lined up.
When the manifold is sitting on the heads with NO gasket it shouldn’t be touching the china walls and the bolt holes in the manifold should NOT be lined up.
The holes in the intake should be lower than the bolt hole in the head.
If the holes line up perfectly with no gasket you need to machine the intake manifold face the thickness of the gasket plus .010.
If you can’t see the hole in the head because the hole in the manifold is too low then you need way thicker gaskets.
If you have to machine the intake make sure you have enough room between the intake and china walls so that when you machine the manifold it doesn’t end up on the china walls.