I'm so smart, I wait until stanbr & JoLui do all the "heavy lilfting" and then I just fill in details on their excellent outlines! (BTW, is everyone else as annoyed as me that when one clilcks "Reply" all previous answers disappear, so one must open a 2nd screen?) Here are some fill-in thoughts(many r also provided by those 2, so I'll save them keyboarding):
HERAKLION -- the Stanbr pair & I have each enjoyed staying Hotel KRONOS, right on seafront, Great to walk along to Huge Fortezza before dinner;; Ippokampus has great Mezedes (Crete supposedly invented this treat - just get multiple meze no mains).
SANTORINI -- Stay in FIROSTEFANI... right on cliff view, but uncrowded, easy 15-min rimside path walk to FIRA. For best experience OIA, get there by 8:30 if poss - 2 hrs to stroll, take pix, enjoy, before tourbus & cruise crowds invade. Avoid sunset mobs, have dinner in Firostephani (Remvi Cafe or Aktaion) or FIRA (many view choice; I like STANI rooftop).
CAR RENTAL - reliable service good rates from Athens-Car Rental; they bring car to you @ airport. Always prudent to walk around car, note any slight "dings" & photo with yr phone. Airport to Central ATH: flat-rate car service about €43; if yr hotel is not far from Syntagma Square, u can take x95 express bus, takes same highway, €6. I often use this when traveling solo.
NAFPLIO - Stanbr pair & I each loved staying Hotel AGAMEMMON if avaialble - only Old Town hotel right ON seafront, yet not Luxe pricing; good back-up choice Omorfo Poli. Of course use superb website http://www.visitnafplio.com/ - click every link! Dont miss sealevel walk around peninsula point (ignore "closed" sign) & drive up back of Palamidi for stunning aerial views. Since u are a true ruins-buff, don't miss TIRYNs right outside of town ... and have your last Greece swim at tiny cove by ASINE (outside of Tolo).
MESSENE & ONWARD - (I concur to not try Mani, & have more time elsewhere) Yes you could get lost for a whole day at ANCIENT MESSENE, it's huuge; but main thing is the breathtaking Wall; read up beforehand on something in-depth llike BLUE GUIDE. If you find u are running out of daylight, u can have delightful eve/overnight in Pylos (the French designed its charming square), or my fave once-unknown beach, little Gialova 10 mi North, Hotel Zoe (they call themselves "Resort" now, but it's same family just pricier).
OLYMPIA - If driving W near coast, as Classics buff, quick stop NESTORS PALACE? -- especially since this amazing 2015 discovery: https://www.smithsonianmag.com/history/golden-warrior-greek-tomb-exposes-roots-western-civilization-180961441/ If u stay in Olympia night before site ... it's not really a town just a looong street of hotels & mediocre cafes. October tour crowds wont be huge, but my hotel's tip istill good: Tours go first to ruins, so if you dp Museum at 9, you'll have it to yourself; it's thrilling. At 10:15 or so, tours pour in & you can leave for ruins; huge area so never crowded. Confusing, advance prep helps... for years, NO downloadable audio guides but now several online. If u get one, for best results run it beforehand , for any glitches.