There are at least two reasons why the larger ports may not seal.
1. Relationship of exhaust ports to the threaded holes for the manifold/header/extractor fasteners varies from head to head.
To account for that variation mass produced headers have oversize or elongated mounting holes in the flanges.
2. TTI and several others don't use the flange surface for the sealing. Instead they run a raised bead around each port. That's easier and cheaper than grinding flanges flat. It also means there is yet more variation possible.
Its going to be time consuming but worthwhile to do a mockup using a transfer marker. The coloured 'grease' used for checking gear contact might work. Carbon paper might also work.
If you do decide to fill in the flanges, try to do the most on the bottom and the least on the top.
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