Hi There
It is possible that if all or most the foam air filter was swallowed parts of it could be interfering with the powervalve operation even stuck in the crankcase itself,for the sake of 2 base gaskets I would certainly be having a look in and around the crankcase,barrel and powervalve area to ensure all of it has blown out and remove whats left before starting it again,
good luck with it all the best,
jonmac
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John