If you continue to have alignment issues on the intake manifold, consider swapping out the standard rings with the adapter rings readily available on eBay and elsewhere that will adapt 216 and 235 port sizes. Here's an example (no affiliation, just an example): 216 to 235 intake adapter rings.

Doug

1947 2nd-Series GMC FC152 3/4-ton
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1953 Chevy Bel Air Sport Coupe Powerglide