Michele,
You've only got about a month and a half to work out the details, so you'll have to get these sorted fairly soon.
To begin with try to find a copy of Europe Through The Back Door at a local Library or Book Store. That will provide LOTS of information to help you work out things like Itinerary Planning. Be sure to carefully read the section on "Rail Skills". You may also want to download the free PDF Rail Guide from this website (click the "Railpass" tab at the top).
Using open-jaw tickets would have been preferable, but if your air tickets have already been purchased, you'll have to work with that.
Which sights do you & your friend most want to see? If you both make a list, you'll be able to narrow down sights that you both want fairly quickly. If you could provide a list it would be easier to make Itinerary suggestions. What are your interests (history, art, museums, or ?).
For such a short trip, I'd suggest keeping locations fairly close geographically. That way you can minimize travel times.
For the most important cities (Paris, Rome), it's a good idea to allocate at least 4-5 days each for those, as there's so much to see and do.
One thing to keep in mind is that you'll lose the first day in flight times, and with jet lag you won't be up to "touring speed" for a day or two. On the trip home, usually you'll arrive on the day you left.
Hostels are a good idea, but it would probably be a good idea to pre-book your accommodations. Although Sept. is technically the "fall shoulder season", I've found in the past that lots of people are travelling and it may be hard to find lodgings. Pre-booking allows a choice not only in the part of town you want to stay but also the price range.
You may want to have a look at the Italy or France Guidebooks, as there's an enormous amount of information there (I usually pack along the Guidebooks for the areas I'll be visiting).
Good luck with your planning!