I loaded your save and it convinced me that some major (not great) powers should be converted to empires. With new release 7.7.5, owning at least 300 territories is enough to become an empire in CK3
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Also, regarding Egypt not being an empire, turns out it was not a bug. Before checking Imperator rank, the converter checks whether the country name contains "Kingdom" or "Empire". Because the name of Egypt is actually "Ptolemaic Kingdom", it will always be converted as a kingdom.
As for other border gore issues, I already have an idea for further tweaks. No ETA, though.