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d_zialcita, sis mahal talaga if you fly all the way to Pisa or any secondary airport in Europe on an open jaw routing. Ideally if you do an open jaw routing it should be with the primary gateway of the airline if not mahal talaga since they will have to add pa the domestic sector fare ng connecting airline which they do not have control with the pricing. Plus hindi pa adjusted yung fares for 2013 since matagal pa yan. Airlines usually come out with the most updated fares 3-4 months prior unless stated in the fare rules nila until when validity ng fares.
Another option for you is to either fly to Milan or Rome (if taking CX or any Asian airline with direct gateways to Italy) then train to Pistoia. There are several direct trains from these gateways to Florence where you can transfer to Nieve Pievole where you'll be staying. If taking KLM, medyo late na rin ang dating since you'll be transferring in AMS, hence the long travel time. Try to compare na lang the pros and cons of either mode of transportation.
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mooncakes and leaves, your IT looks good except for Day 3. Here are some comments:
Day 1 - Unless you made online reservations do the Eiffel Tower either first thing in the morning or last thing at night since the queues here are humongous. Walk to the Trocadero across the bridge in front of the tower where you can get the iconic view of the Eiffel. Either take the metro to the Arc de Triomphe or just walk it. Walk along the Champs Elysees towards the Louvre (medyo malayo ito), a better option would be to take the metro and get off at the Louvre. If you get the Paris Museum Pass you don't have to join the long queue at the Pyramide entrance. Go straight to the Richelieu entrance where pass holders have their own access to the Louvre.
If you're not too tired with all the walking, then head off to Sacre Coeur.
Day 2 - Yup, do the Notre Dame first thing in the morning since this is another popular tourist attraction. If you want to climb the towers, try to be in line by 8AM (facing the church the line would be outside to the left). As soon as you're done go inside the church to check out the pretty Rose windows (line is in front of the church).
Back outside in the square if you're wondering why a lot of people are looking at their feet taking pictures, that would be the Paris Point Zero marker from which all distances from Paris are measured.
Walking towards Ste-Chapelle you can drop by the flower market at Place Louis-Lépine. It becomes the bird market every Sunday.
At Sainte Chapelle, there is no special entrance for pass holders. You will have to queue with everyone to get through security since the chapel is located inside the Justice compound. Once inside ignore the long line and go straight to the entrance to show your pass. The long line would be for ticket buyers.
At the Shakespeare & Co. you can buy a book and have the cashier book stamp it with their logo.
Day 3 - I'm afraid this is too much to do in a day. The catacombs you can squeeze this on Day 2 just after Sainte Chapelle. So you can still have your sunset at the Shakespeare and Co. sabay mag-river Seine cruise ka if you want. It's another way of having an overview of Paris.
To get to Versailles take the RER C (suburban train). It's usually a 45 minute train ride. Do the Chateau first then the grounds. If you get there at 9AM, you can be done by 2-3PM and back in Paris by 4PM. If you weren't able to do the catacombs day before baka masingit mo pa dito if you're not too tired.
Day 4 - Good idea! Hubby and I just love wandering aimlessly here. Sabay shopping!!!

Lastly, get a bottle of local wine and a baguette sandwich and picnic at one of their lovely parks and just relax and enjoy the Parisian way of life!