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By the way how would one go about linking these unattributed coins and dies to the Aegai mint or even to each other would be good enough for me at the moment.
The short answer is, "archaeology". Archaeologists attribute coins of unknown origin to mint-cities based on find evidence. If coins of type X are frequently found in or in a radius around the ruins of city Y, then it can be said with confidence that city Y made the type X coins. One can make logical deductions until the cows come home about where the mint "should have been", but if there's no evidence on the ground there, it does not become an archaeological fact. I assume for the coins in question that the evidence simply isn't there; either the coins are rarely found or the evidence is so ambiguous that no conclusions can be made.
One should also remember that mints were in theory a lot more "portable" back then than they are now. All you needed were the workers, some basic tools and a room which could be (temporarily) secured. Both Philip and Alexander were warrior-kings, spending much of their reign on the march. They may have taken their mint, or at least some of the mint workers, with them, as some of the later Roman emperors did. If the same coins were struck from the same dies in different places, that can throw plenty of confusion into the archaeological record.
Don't say "infinitely" when you mean "very"; otherwise, you'll have no word left when you want to talk about something really infinite. - C. S. Lewis