I expect you mean May-June 2013. But if you do happen to have a time machine that goes backwards, could I borrow it to fix a few of my more silly mistakes?
I did the first route you mention as part of my European tour in 1984-'85 - only place on your list I didn't go was Toulouse. I highly recommend this route. Not sure how my experiences nearly 30 years ago relate to the present day, but one thing that won't have changed is the scenery, which will be fantastic.
I would urge you to fit the coast of Yugoslavia in there somewhere - it's incredible!
Buying a bike in Greece may pose some problems. 28 years ago, Greece didn't have many bike shops, but things may have changed. If I was doing a similar trip based on my experiences back then, I'd probably get my bike in Trieste, Italy. Then I'd go through the old Yugoslavia, see Dubrovnik, ferry to Greece, then do a bit of day-cruising (ferries were dirt cheap back in my day - maybe a bit more expensive now), maybe a train or ferry to Istanbul (everyone should see Istanbul, but getting there from Greece by bike takes a good few days and with little in the way of interesting places to visit), ferry to Brindisi, then back on the bike through Italy to the south of France, Carcassonne, across the Pyrenees to Barcelona. Of course, I've just added a thousand or more miles onto your trip.
Places to miss - there's a flat plain between Bayonne and Bordeaux. I cycled it and it's mind-numbing. I seem to recall a perfectly straight road for 80 miles with nothing but the same kinds of trees either side. If I was re-doing the whole trip, this is another place I'd get a train. Better still, head farther east towards Toulouse and head for the Dordogne.
Your second route looks good too, though I've only been to 7 of the places you mention.
The first route seems a bit more adventurous, but you shouldn't worry about safety too much. Even 30 years ago, all the places you mention were perfectly safe for anyone to go alone.
I'm no gearhead, but I would advise on getting a long-wheelbase touring bike (or a hybrid) for the trip and some good kevlar tyres. North of Greece, roads are always pretty good, and even the Greek ones aren't too bad unless you're up in the mountains, where rock falls can take out roads (I once had to double back 20 miles because of this in the Pindos).
Highly recommend Youth Hostels, though prices may be a lot higher than they were in the 1980s. North of Greece, they are (or at least they were) spaced very nicely for cycling. Major cities have unofficial hostels that are as good as the official ones, but many are more laid-back, co-ed, and have bars and a party atmosphere. Places like Balmers in Interlaken, the YoHo in Salzburg (where I worked for 3 years and where I met my wife - we on the staff used to call it the Hotel California, because, like the song, it's a place that you can never leave - though it's a bit tamer nowadays), and numerous party hostels and cheap hotels in Athens and Istanbul.
