Two weeks? Are you nuts'!
Why not three or for or 3 months?
What do you have to rush back to?
Seeing Europe is worth more than just a quick peek.
Like Rick Steves says, "Europe is more than just historic sights and museums. Its the people you meet."
Aand by meet we mean time for in depth conversations. That´s what youth hostels and trains are for.
You should read "Europe Through the Bacxk Door" very soon.
It helps with planning, security (serious stuff, though its safer here than stateside.) planning, and stuff he can´t cover in an hour show, or we could think of here.
This Texan lives in Seville.
If you get a train pass
: The way I measure a day´s travel, is by where we get by 6pm. That way I can find a room, before their all full.
It lets you see those out of the way places.
History happened everywhere.
Be sure to visit town museums. They aren´t about covered wagons and WW1.
They´re about the iron age or late stone age.
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Eat at little mom and pop cafes, up in alley ways. They´re where the locals eat and they´re cheap.
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THE MOST VALUABLE TRAVEL IS DONE WITH THE EARS.
One objection to us yanks is, "They only talk to the people they travel with."
Lets fix that.
WHY NOT GO HOME A LITTLE WISER THAN WHEN YOU LEFT?
Could you tell us your thoughts on what's been posted here, so that we know it's been in any way useful to you? There have been a lot of very extensive,labour-intensive replies here which raised some more questions as well. Would be nice to get detailed feedback from you.

I would replace the trains for planes (only for London - Paris, it would be good if you can get the cheap seats on the Eurostar). I would choose a maximum 3 cities (e.g) London - Paris - Madrid) for Paris - Madrid you could choose to fly Vueling Airlines (I think it is the cheapest option)
Chueca is 'the' gay area in Madrid (like someone said before), but you will find gay-friendly bars all over town. (it is a gayfriendly town in my eyes) I do prefer the Lavapies / La Latina area.

With all the help I've gotten thus far, I've been drafting up an itinerary that looks like this:
WEEK ONE
DAY ONE: Depart from Chicago, IL to Pisa, Italy. Depart to Florence by train.
DAY TWO : Florence
DAY THREE: Florence (Day Trip to Rome?)
DAY FOUR: Depart Florence to Venice in the afternoon.
DAY FIVE: Venice
DAY SIX: Venice
DAY SEVEN: Depart by train (overnight) from Venice to Paris, FR. (I hear I'd have to take a train to Milan then from Milan to Paris?)
DAY EIGHT: Arrive in Paris, FR.
DAY NINE: Paris
DAY TEN: Paris
DAY ELEVEN: Paris (Day Trip to Versailles)
DAY TWELVE: Paris (Day Trip to Giverny)
DAY THIRTEEN: Depart from Paris, FR to Madrid via train (overnight).
DAY FOURTEEN: Madrid
DAY FIFTEEN: Madrid
DAY SIXTEEN: Depart from Madrid to Miami, FL.
DAY SEVENTEEN: Back home!
Any flaws so far? Too many day trips, perhaps?
So far we've decided to spend at least another week on vacation in Europe and save at least another 1000 to 1500 bucks. Our parents are chipping in and buying our plane tickets so that's one less expense we have to worry about. We're cutting out going to London as we both decided would rather just save that for another trip, same goes for the Ibiza idea. Instead of Going from Paris to Florence, I thought why not switch it around and do it the opposite way. And should we really fly or is it okay to go via train? Is this a bad decision or should we really stick to cities that are relatively closer to each other rather than country hopping?
Also, I was curious to know if maybe we could opt for a rental apartment/studio as opposed to staying in hostels/hotels everywhere? I think it would be a nice break from that and provide us with somewhere to cook to save on costs too? Has anyone tried this on a budget and is it possible?
I do appreciate the information on guidebooks, I am definitely picking up a copy of Rick Steves, I was also wondering if the Time Out Guides are any good? Same for the information on gay friendly places and everything else.
I'm trying to streamline so we can do and see thing we really want to see while enjoying the trip and not spending too much. Are there places that we could afford to see the next time we travel to Europe? My partner wants to do EVERYTHING and I just want to mellow around and enjoy our trip and the time we get to spend together, so this is one of the reasons the trip is ALL over the place.
Again, thanks for the help. It's doing me a world of good and I'm so excited to continue planning all of this, especially with all the help I've gotten from you all
Ahhh, you're back - that's good. Your reply at #13 was a tad brief! It's great that you'll have an extra week but I don't see where you've added it to your original two weeks. All I can see is 17 days. Never mind, I'll try to answer some of your points.
Dropping London and Ibiza = excellent idea.
DAY THREE: day trip to Rome = very bad idea IMHO. The train journey takes 1.5 - 2 hours. Now add the time it takes to get to Florence station in good time to catch your train, finding your bearings in Rome, then getting back to the station in Rome...I reckon you'll spend 5 - 6 hours all told on just getting to Rome and back. It hardly seems worth it to me, hard work even, especially when there's some much to see in Florence. For me a far better idea would be to make a trip out to Fiesole.
DAY SEVEN: currently there's one direct overnight train from Venzia Mestre to Paris: dep. VM 20.19, arr. Paris Bercy 08.23. No need to change. See the link to the German Rail Service below. That's great because it gives you all of Day 7 in Venice.
DAYS ELEVEN/TWELVE: I agree with you that you might be taking on too many daytrips from Paris. Unless you're the kind of people that just want to visit the big tourist attractions, rather than the citires themselves (much more rewarding and interesting) you'll find loads to do in Paris, especially when you really get into your background reading. It's a really fine city. I'd leave myself some flexibility there not not plan ahead too much.
DAY THIRTEEN: I've always wanted to take that overnight train from Paris to Madrid. I've read so much about it and it sounds a really great journey, much more atmospheric than schlepping to and from airports. One flight is pretty much like any other - this train journey is really special as experiences go. See if you can talk your folks into contributing to some nice on-board accommodation for a real treat; it will be money well spent. Scroll down this page to the part about the "Francisco de Goya" trainhotel (in Spanish trenhotel) and you'll see what I mean.
If you do finally end up with more than 17 days, I would add them to your Madrid stay. Plenty to see and do plus some great day trips to make to places like Toledo, Segovia, Aranjuez, and so on.
Oddly enough perhaps, one of the best websites for rail travel around Europe is the German Rail Service. Enter "Venezia Mestre" against "From" and Paris as your destination. Just enter a fictitious date (like tomorrow's) to get the current timetable.

Essentially, I'd like to add in those extra four days somewhere in Italy but I wonder if those days would be better spent in Barcelona?
And on the day trips, I just think we've got to come to a meeting of the minds on that front. I really want to stay in the cities, wander around, eat and just enjoy being there meanwhile my partner wants to see every touristy/artistic monument possible. The more we talk about the trip, the more I think she realizes the experience will be much more than just hopping from gallery to gallery and from church to church. I personally would love to see Versaille and she really wants to go to Giverny for Monet's Garden so I guess we'll just see how all of that plays out.
As for Rome, I think it would be better to do Rome on a different trip. We are interested in going to Greece in the near future so perhaps we'll just see Rome then.
Sorry I didn't give a full reply sooner, I just wanted to let everyone know I was peeking in and taking your suggestions to heart.
As for right now, my parents are taking care of our tickets so that's one less cost to worry about and I guess the money we would have spent on airline tickets can go towards the Paris-Madrid overnight :)
Thanks again!
Personally I think it would be unwise to add yet another destination to a list that is perilously close to overload for the time you have available. It adds a a fair amount of extra travelling (cost + travel time) and you'd lose two of those days getting to Barcelona and then moving on to your next destination.
I just think you would be better off spreading those four days between the places on your existing list. For example, Madrid is crying out for at least one extra day, as is Florence. You could make an easy daytrip out from Florence to one of the many lovely nearby Tuscan small towns to take up that extra day.
I really would use those extra days to add an extra dimension to your stays in the places on your list rather than skimming the surface of Europe and spending a couple of days in yet another city. It's more relaxing too. Bear in mind that all of those cities are far more than just a collection of well-known sites: they're organic places where people live and work, often with little treasures off the beaten track. It's quite easy to escape the tourist hordes and it can be immensely rewarding to do your own discovering but that takes time.