Buy a good map of Europe (Michelin makes one and many bookstores carry it).

Cut a post-it note into smaller pieces, and mark each of the destination you have listed. Then you should be able to find the best path to get where you want to go.

I wouldn’t lock myself into a round trip ticket, because that means you have to spend time and money getting back to where you first landed. It often makes more sense to get a multiple-destination ticket (they are also called open jaw tickets, but most of the web sites that list ticket prices use the term multiple-destination) where you arrive in one place, but fly home from another. Be aware that you are going in what they call the high season, where prices (for everything, including flights) are generally higher; you are wise to avoid August, as it is hectic with most of Europe going on vacations, and no one left to run anything.

I avoid the low cost carriers in Europe; they often have unbelievably low fares, but often use secondary airports, and are famed for there limitations on how much you can carry, so if your luggage is a half-kilo over their limit, you get hit with an excess baggage charge that can often far exceed what you paid for your own ticket.

Only you and your friends can decide what sites you really want to see; I often visit a small village in Switzerland because my ancestors came from there; other people wouldn’t find it interesting at all.

All the places you list seem interesting to me, but I would ask why Interlaken? It is not in the mountains and I don’t think it is particularly attractive, but some people say is is less expensive and you can easily take day trips into the mountains from there. My preference would be the nearby town of Lauterbrunnen, which is nearby, but in a scenic valley that can be walked, and very convenient to some of the mountain villages. If you want something very scenic, but very quiet, stay in one of the mountain villages above Lauterbrunnen.

I wouldn’t delay in planning this trip. Airlines have cut back the number of flights, and who knows what complications will be added by the actions of the underwear bomber? Have a firm plan, with everyone in agreement, so that one person can act immediately when a great fare shows up, as on a sale, as they are sold out quickly.

I’d recommend saving Greece for your next trip. You’ll spend at least a day getting to Athens and at least another day getting to your next destination. IMO, Athens is worth a day. If you don’t have time to spend at least a week in Greece, don’t spend the time and money to get to Athens. While I love it, the same is true for Croatia. Unless you have a week to spend in Croatia, Slovenia, and surrounding countries, don’t take the time to get there.

An open-jaw fare is not a bad idea, but it’s understandable that you might want to go ahead and lock in that $554 fare and be able to know that your ticket is bought and that you got a good deal. I’m not a big fan of backtracking, but with 50 travel days it’s not as big a deal to lose some time getting back to Dublin, and by booking your flight back there well in advance it should be cheap. Definitely note what cleavelandbrown said about the low-cost carriers, but I wouldn’t completely rule them out. Check what they offer versus other carriers for each leg of your journey and decide on a case by case basis.

$554 is a great fare for that time period and I would go ahead and lock into that.
IMHO you have enough time to make a nice loop, and low cost carriers in Europe can be successfully utilized.
However, I agree with Oldlady that Athens deserves a day and transportation in Greece (and Croatia) is time-consuming. If you do venture into that part of Europe, you will need to devote more than just a few days.
With a bit more research (and decision-making) I think you can figure out a cost-effective itinerary.

@alymarie: You can drag and drop the cities in your itinerary to change the order to find the best route. Once you do that, specify which legs you plan to fly with the drop downs and the days in each city. Then click on ‘Find the best Railpass’ and it will find you the cheapest railpass(s) for your trip