Don't worry. You'll be fine with the driving and the tolls are not excessive.
I would start with Meteora (since Delphi is closer to Athens and the most important thing is to not miss your flight). Get a start at a reasonably early hour and you could be arriving at the monasteries by, say, 1 pm. (From a central hotel it's going to be 4.5 hours, at least, to get there). Visit two monasteries (hours are easy to find online, one will be closed on any given day), return to Kastraki, check in to accommodations, relax with a drink, then maybe head back to the high rocks for sunset photos (sundown 7:45 pm).
Next morning, visit the monastery that is closest to town (I forget the name but it will be obvious which one I'm referring to - skip this on Day 1, do it on Day 2 as it will give you a quicker getaway), drive to Delphi. This is 3.5 hours, minimally assuming you don't miss any turns but the fastest route can be a bit windy (don't worry, there won't be any traffic, at all, and it's quite scenic). Don't worry about arriving in Delphi a little late, though, because there's really only two things that you'll be doing. I would visit the museum first and then the archaeological site second. The site closes at 8 so if you were to arrive there at 5:45 or so you'd be in great shape. The museum on some days closes a lot earlier than the site, that is why I'd see the museum first. Meaning, let's say you arrive at 2:30. Visit the museum, finish at, say, 4. Walk back to town, check in to hotel, grab a bite at a scenic taverna. Head back to the archaeological site by 5:45 and you're good.
Now, if you have an 11AM flight from many places in Greece I'd insist that you stay in Athens. But, from Delphi you will skip the urban center of the city via a high-speed freeway and get to the airport easily. Keep in mind you'll need time to return your car. I would be on the road by 6AM if you stay in Delphi, though, so a missed exit won't kill you.