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I had a similar issue way back when after I "gutted" my stock LT1 Aluminum valve covers to clear after market rockers. I ended up using the same method you did with the Permatex and it turned out to be the valve covers flexed when I cut the supports out and I needed to massage the cover lining inwards (if that makes any sense, it was the channel where the gasket goes in and over a center bolt style cylinder head)
I ended up using a small hammer and a good piece of wood.
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