Here u are with bookings made before askin for feedback, so if we have a tweak to suggest, it's not possible. You say arrive Heraklion 10:30 pm. I assume you are flying there. You must LEAVE from Heraklion, so why not fly in to Chania?... that way no backtracking. As it is, you don't have time to even glimpse Chania, the 2nd-most-beautiful Old Town in Greece (next to Nafplio). You really only have TWO days in Crete -- (and the first day you'll be fairly jet-lagged) ,,,and you can't wander far from Heraklion, if you are going to make that 9:45 AM ferry to Santorini. SO...
DAY 2 (night really - it's 10:30pm at airport -- Taxi from there but you won't get checked in until 11:30-12) Try for a room at Hotel Kronos, on the seafront ( ... Hotel or Lato, a boutique hotel if you like fancy, but y ou'll be too conked out to notice).
DAY 3 (which actually is day #1 of your actual time in Greece)... Drag yourself out of bed & go at AM to Heraklion MUSEUM... and in afternoon go to Knossos -- the cruise-ship & package-tour crowds leave by about 3pm. There's a public bus right by the ferry pier that takes u right to the Knossos gate, in 30 mins; no need to rent a car in the madness of Heraklion traffic. Go back for a nap, walk out on the causeway to the Stunning Fortezza, then have a nice dinner right at the foot of the causeway, at Ippocampus or Ligo Krasi ... of "mezedes" (small plates), which are the Cretan specialty... you'll each get 3-4, lots of variety, at a bargain.
DAY 4 -- Rent a car for the day??? (you need a Intl Driver License for this; go to any AAA office, get one in 20 mins). There are several options (1) --- drive WEST on the big north road, just for the scenery.. a sfar as Panormos, then go inland about 10 miles to MELIDONI CAVE -- beautiful insides, hauntng & poignant tragic memorial (A turkish massacre in 1825) (2) Drive south to Scenic (and restored) Epano Arhanes & town of Peza in heart of Wine country, & visit a couple of vineyards. Either one would get you out of Heraklion -- if you were going later in the year, you could do a bus excursion but I doubt any would be offered in April. I suggest you ask Hotel desk about a vineyard & village they'd recommend. That way, you'll be in Heraklion hotel that night & the next AM, right near the dock for your ferry.
... as for the rest, I see you are limiting Naxos in effect to 1 day in favor of the Mykonos shopping experience, so I'm done here.