Well, the time period matters a lot in terms of culture/technology and NPCs. If you're going for the era of Thera's actual explosion than everything is going to be pretty speculative, keep in mind that we still haven't translated a lot of the record keeping systems from that period and our only historical records thus come from later myths and Egyptian records, which are always notoriously inconsistent.
And now for the wild speculation:
First of all, read Mary Renault.
Second, keep in mind that many Greeks believed their gods were versions of the Egyptian gods, Herodotus in particular, so that your divine conflict formenting an Egpytian invasion has the opportunity to have another more complicated side to it.
Third, Crete during the period of Thera's explosion and for sometime afterward was dominated by what Archaeologists have termed, at least in my limited knowledge, the palace or big house system. The way this worked, from what we understand, is that Crete and the environs of Minoan civilization, were dotted with these huge and unfortified palace complexes into which loads of goods flowed on a very regular basis and were carefully tracked. This system survived at least one major disaster and an invasion that entailed a linguistic shift.
We know they made a lot of documents that appear to be contracts, that they traded widely-thus the Egyptian accounts, had a reputation for being fierce foes of piracy and for heavy tribute, that the palaces apparently had religious significance, that women were highly honored, that the Minoans used a lot of art and some fairly advanced construction tech in the big houses, and that the Minoans are consistently thought of in Greek culture at large as having very strange religious ideas and a lot of isolated power. In Homer's list of ships the prince of Crete brings one of the largest group of ships and is the most neutral and calm in the divisions in the Greek force.
The religious reputation is consistently seen as related to Minoan culture because it differs in very telling ways. The Cretans got a reputation for being liars, for instance, because they claimed that Zeus was constantly coming to their island to die and be reborn, a tale that was totally inconcievable to the immortality based theism of the mainland. There are also all the references to bulls in Greek myths about Crete reflected by a Minoan obsession with bulls in their art.
There is a lot of wildly varying speculation about Minoan government. We do know they moved a lot of goods and kept extensive records in their seats of power, and that they sent embassies all over the mediterranean, not only are their artisitic representations and written references to Minoans in Egpyt, but there are also Minoan murals depicting conflicts with people who could be sub-saharan Africans and were at the very least Western Mediterranean North Africans.
The speculation ranges from theories that focus on the myth of Crete's scientists and scientist kings: Minos, Rhadamanthys, Icarus's dad, and so forth. To theories on Crete as the last great matriarchical state representing the greatest manifestation of the original female ur-religion of the European continent. To theories on Crete as essentially a modern state married to religion with a strong beauracracy, an advanced permament military, strong international alliances, some ethnic diversity and immigrants, and an extensive spy network. To utopian dreams of Crete as the ultimate pacifist state with lots of opium smoking and art work. All of these have some undeniable evidence behind, none can be shown to be utterly superior, the record is just rich enough to support them without being complete enough to weed any out.
The most sedate speculation is on how Crete may have divided itself during the palace system into rural highland and coastal urban areas that were united by the ritual life of the palaces and that all hell broke loose in the tensions between them when Thera went down.
Oh, Terry Gilliam's Time Bandits features a scene set during the Greece of this periods later moments. An excellent visual aid.
So, for this period, NPC wise, I think you might be looking at scholar/scribes for the palace records, captains of men and ships, representatives of the two Cretan peoples, a ritual priestess of the palace, mystery priests of the specific deities, a scientist, a foriegn mercenary or two, a foriegn diplomat, a Minoan diplomat, a representative of the matriarchy, an artist, a scientist king, a merchant-explorer, pirate convicts, sailors, and tribute slaves.
Not to mention various monsters such as the great golem, minotaurs, nymphs, and cyclopeses of Crete. The nymphs of Crete were particularly important as they cared for and protected Zeus during his infancy. They are, interestingly, characterized as extremely militant.
Specific characters from this period can easily be drawn from mythology. Basically anyone from the Argonaut series of myths and earlier could easily be rewritten for your chronicle. Given your particular interests I highly recommend working with people like Orpheus and Pythogoras who founded Greek religious institutions and had, therefore, loads of magical power.
If you wanted to mix time periods I think you could easily do classical Greece at some of the Cretan ports and much of the mainland and Minoan mythical Greece on the islands, a few Cretan ports, the highlands, some of the mainland city states, and most of the weird mainland village areas.
Then you can use characters from all the periods and have a nice conflict between the cultures, where the myth/minoan culture has the magic and high tech and the classical Greek culture has iron, horses, many strong deities, and numbers. Athens would be a meeting point of the cultures, having been independent of Minoan soverignty for some time and adopted the new gods, but still being a people of the old blood.
The conflict doesn't have to be active mind you, just everyone's aware that their is the old culture and the new. A situation that was present at many times in Greek history.
Oh and, regardless of the speculation, Crete the palace system probably had a strong executive, read 'king,' during part of its history. Knossus features a throne room that was probably the ancestor of every European throne room in history. Big immovable chair on a dais in a fairly small audience chamber. Kind of hints at someone being the focus of attention in the palaces.