First off, don't worry! It's not like you're trekking through the outback. No matter how "horribly wrong" you plan things, it can't go that badly. Western Europe is the easiest place in the world to be flexible in your travels. I planned a weekend trip to Donostia once, accidently boarded the wrong train and fell asleep, and woke up in a city I knew nothing about hundreds of miles in the wrong direction. I just found a hostel, made do, and had a lot of fun.
Second, be careful! Two very young women traveling together is better than one traveling alone, but still you are in a bit riskier situation than guys would be. Stay out of poorly lit, lonely areas, ask your hostel/hotel staff what areas and businesses should be avoided, and if a situation starts to feel even a little bit wrong, trust your instincts and get out of it immediately. DO NOT worry about offending anyone.
Now that said, your itinerary does look a bit ambitious for three weeks. Don't forget that every time you take a train, you'll be spending some amount of hours traveling between places. Even if the trip is short, getting to the station, waiting for the train through the inevitable (in Italy) delays, then finding your way to hostels from the destination will eat up hours. Only a couple of those trips are long enough that you can do the sleeping car thing. If you plan to spend most of your time in Italy, you have a good set of places to visit there over the course of two or three weeks, plus you should add Florence next to Pisa, which is really daytrip material from Florence anyway. Pompeii is also more of a daytrip from Naples than a destination unto itself.
Geneva and Paris are both worthy of a whole week's visit. The idea of doing both of them, then a couple other countries, in a week I think is far-fetched. So your Italy leg is good, but once you leave Italy I think you've planned far too much, especially since it's the shorter part of the trip.
A thousand pounds is a very tiny sum for first-time travelers. Figuring an average hostel rate of 32 euros (£27) per night each, that's already 57% of your budget gone (and you'll be lucky not to go over that, since it's not always possible to find a hostel and you might end up at an expensive hotel). You've got to eat a little bit every day, so that's a minimum of another 20%, and that's buying bulk at markets and having the discipline to avoid all of the delicious restaurants you'll find in Italy and France. A lot of the amazing sites you want to visits have entrance fees that can range from 5 euros (token cost for a museum) to 40 euros (for things like a daytrip to Pisa). Figure in also for transportation within cities, where you'll be spending a couple euros every time you take a bus or metro, and confronted with the temptation to take taxis on those longer trips from train stations to hostels. And speaking of trains, are those tickets already paid for or does the £1000 have to include that? What about reservations? It's becoming more and more common that reservations are required, even on shorter trips, that you'll have to pay for as you go.
In sum, I would personally worry a lot less about you if you had 30% fewer destinations and 50% more money. Stick to Italy and Geneva or Paris, and try to save £1500 each. You'll have a far more leisurely trip, and not have to worry about the occasional nice meal or cab ride.
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