Alex, I know you're going to have a wonderful time, and I believe you posted before, and your boys are enthusiastic about Greece. May I respectfully inquire whether you've acquired an actual guidebook to aid your plans? If you're spending well over $10,000 (14 days w a lot of transport costs, + 4 RT USairfares), a book really is worth a few $.... trying to do it all on the internet is the worst kind of economy. Steves guide is good for ATH & mainland basics (plus I llike his DIY of Acropolis & Nat. Arch Museum), but I always also recommend ROUGH GUIDE to GREECE because of its comprehensive coverage of culture, history language food etc ... AND the bonus is, you can carefully pull apart the sections u will need, bind spines with duct tape & Presto! pocket-size "guide-ettes"! Many of your questions will be answered just with a bit of browsing. Let's run thru some of your list (and I'm basing this on my 12 extended trips in greece, 9 of them taking along 3-4 "newbies" to major destinations) --
TIMING & MUST LIST - Guessing that your dates include arrival & departure days -- so really only 12 days. In addition, your days will be shorter than in summer, and given the Greek economic crunch, some sites may still stick to shorter winter hours (closing at 3) Be prepared for one-nighters, and even so, you simply cannot do your whole list, mainland OR island. You'll have to leave out Meteora. And probably Olympia which is NOT a day trip from Nafplio (but NEMEA, a superb "sacred games" site, is a great substitute for the latter). To do Delphi w.o. backtracking, link it to your Athens stay. Here's an attempt.
DAY 1 - Arrive (tired!) @9:30 USAir nonstop. Coffee! Car rental, Destination Nafplio. 10 miles after Corinth Canal Jump off big intercity hiway to NEMEA -- Glorious!! Ruins, stadium!! (1 hr) Bite to eat, then on to NAfpllo, crash for nap, enjoy sunset & Early night! Here's a quickie view of Nafplio joys - https://www.flickr.com/photos/stanbr54/sets/72157632094108982/
DAY 2- 3 - Explore Nafplio (MEMORIZE this site!! http://www.visitnafplio.com) .. castles, forts, Museum + Tiryns + Mycenae etc
DAY 4 - Leave early; Epidaurus ampthitheatre (skip rest of site), at Isthmia, jump off biggie highway for photo op on Old Bridge above skinnnny deeeep canal. To airport, drop car, fly to Santorini arrive late day, sunset & dinner.
DAY 5 - Santorini ... Views, Museum, Akrotiri (car rental).
DAY 6 - Island #2 (I urge NAXOS instead; Milos will be deadddd off-season). the 3:15 Blue Star Ferry (2 hrs), large ferry w. open decks is a great "mini-cruise" experience. Stay at Beach (St. George) adjacent to town, lots going on, shops, cafes etc.
DAY 7 - 8 Explore Naxos town (forts! Ruins! winding "Maze" streets); day 2 rent car, zoom all over island, ruins, marble quarries, mountains, beaches -- great stuff for boys to discover. Photo sample https://www.flickr.com/photos/stanbr54/sets/72157634605629689/
DAY 8 - FLY back to ATH Airport (reserve NOW! only 1-2 flights, small jets) Rent Car, drive to DELPHI 3.5 hours for sunset/o-night -- if museum still open, can see in afternoon, also non-fenced part of ruins (Tholos tomb). Recommend Pan Hotel, mountain views.
DAY 9 - Ruins at 8 AM & museum, before bus-tour crowds arrive. By noon, drive back to ATH (3.5 hours) drop car at airport get Taxi (flat rate €38) to Hotel in Plaka. If still peppy, start your sightseeing by going up Acropolis 5 pm, for golden sunset on stone.
DAY 10 - 11 - 12 - Finish ATH sightseeing! This website http://www.athensinfoguide.com/open.htm lists many FAB museums & sites your boys will like (Musical Instruments etc).
This is REALISTIC, use-tested ... plenty of time for boys to run around, and relax-time in sunset cafes, too. If you cram in more, you'll enjoy it less, I promise you.