It’s impossible to know what combination of pass, passes, point to point tickets, flights and buses is best without an exact itinerary — exact places, dates and times for every single trip. If you have that kind of itinerary then about 150 hours of on-line research on the individual national rail company and budget airline websites will probably get you the best deal assuming you’re willing to buy a non-refundable plane or train tickets well in advance for any special low fare that you find.

For a best guess, I’d look at two 3-country select passes covering France, Austria and Switzerland — probably 8 or 10 days for each of them depending on how many 1/2 day or longer train trips you think you’ll take in 3 months. I’d validate one pass when you arrive and use it for any trip in those countries where the cost of the ticket (or total cost of the tickets if you’re taking more than one train that day) is more than the average price per day of the pass. After that’s used up, or the 2 (not 3) month validation period is over, start doing the same thing with the second pass. I would fly to/from Greece and use ferry (IMO, the islands are what you want to see in Greece) and the occasional bus or point to point train ticket within Greece. I would buy point to point train tickets for trips inside Czech Rep.