Well thanks to a fellow FABO member
@416stroker it's obvious now why I couldn't get it to seal. It's not a simple issue of my methods being wrong because like I said I've swapped intake manifolds on small blocks at least 10 times and only ever had a sealing issue on this engine. It turns out the underside of the intake manifold on that passenger side front corner doesn't have a wide enough "flange" to seal up against the block and head in that area with this specific combo of parts. The pics he shared with me explain it all...
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What's odd is I once ran an RPM Air-Gap on a 360 LA block with factory iron Magnum heads and didn't have this issue but maybe I just got lucky or didn't notice it as much lol. Oh well at least now I know!