Travel in Europe by Rail for 3 months

Just remember that you are limited to 90 days and not three months in the Schengen zone. 3 days should general be enough and you know that there is a fee for the reservation. In France the number of seats for pass holder is very limited so early there should be at least a couple of weeks.

Thanks for the information, our trip will be 3 days short of the 3 months. We also thought of getting a Visa to stay longer.
The train reservation is my main concern since I have hotels booked for the whole trip. Wish me luck!!!
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Bookings are available anything from 90 to 180 days out, different companies have different times.
Seats are usually available 3 days out, but I would go for 3 weeks+, especially in France where there is a quota for pass holders.

Timetables change every year on the second Sunday in December, this year 13th December 2015. Timetables for next year are not available yet. Every year this causes problems as people want to book early for the Christmas and New Year period, but sometimes timetables are not finalised until November, so you cannot book until then. Some railways also do minor changes in July.
But, for planning, just assume the times are as at present.

Have you checked the weather, especially in December and January north of the Alps (Germany, Northern France)? The weather at this time can be very tourist unfriendly.

First, for each of the countries, the rules and availability change greatly. Do some research and the differences will become apparrent, for example, as was mentioned, France is both expensive and limited...Italy, good availability and not too expensive, Germany, most trains you may not even need them.

I would also at least look at alternative options to the high speed trains. In each case a regional or intercity train going the same route, though slower, still gets there within an hour or two Also keep in mind reservations required, vs optional. On German trains, a reservation often is not required, you just are not guaranteed a seat (nearly always something is available) even then, you can still catch the train, you may wind up standing or having to switch seats as reservations fill for segments.

Do you mean your time in the countries you list will be 87 days or 89 days? Day 1 is when you arrive and get your passport stamped at the point of arrival. The last day is when you fly out for home. Please note that any part of a day, counts as a day. So 89 is cutting it pretty close. It's a good thing to be thinking in terms of the 90 days, not 3 months.

We will be going across and back on Cunard arriving in Southampton England and catching the Eurostar on the same day to Paris so that would be our first day in Europe since England is not considered being in Europe. We plan to be back in England on January 3, 2016 which will be ample time to be out of Europe.

In addition to the quota for pass holders, we have been told that the pass holder reservation option is deleted from French computers 3 days before departure of the train. That's an additional reason to try to book TGVs about 3 weeks in advance, instead. These should be for sale at train stations in other countries, or Rail Europe sells most of them as e-tickets.

You won't be traveling in peak tourist season, but the trains are well used by residents and France seems to be grouping rail pass travelers into the same "bucket" with advance-discount ticket buyers. Thalys trains from Paris to Brussels and beyond have similar issues. Spain's fast trains also impose some pass holder limitations, but I have not heard a complaint about it for a few years.

See also http://www.ricksteves.com/travel-tips/transportation/trains/reservations.

First of all, carefully consider if a rail pass is what you really want. Short of buying full price first class tickets, it's usually the MOST expensive method of travel by train in Europe, and the flexibility it once offered has increasingly vanished throughout the years... and if you're asking about reservations, flexibility couldn't be that much of an issue.

" I see that reservations on high speed trains are required and they advise us to book early." I'll only comment on the rail services in the countries I know on your list. Reservations are not required for ICE (Intercity Express) trains in Germany. They are useful mainly so that you don't have to fumble around once you enter the train to find a vacant seat, but hardly necessary. The reason to book early is because you can save a lot of money if you can commit to riding a specific train in advanced. But this is irrelevant if you waste money on a rail pass. Even at the most busy times of the year, you can find a seat somewhere on the train without a reservation, although not everyone in your party may be able to sit together.

In Belgium, there are no seat reservations on domestic trains and no advanced purchase discounts. There is no cost or convenience advantage to doing anything other than buying your ticket at the station immediately before your train leaves. One expection is the Thalys high speed service, which links Paris, Brussels, Antwerp, Rotterdam, Amsterdam, Aachen and Köln. This service works more like an airline. A ticket buys you a specific seat on a specific train, and you save money the earlier you book. Pass holders must purchase a hefty supplement to ride on these trains.

89 days is fine. BUT if you fly into Rome (or anywhere else, but our experience was Rome) be SURE you get your passport stamped at entry. The officials in Rome are lazy and we were just waived through without a stamp. when we were leaving from Amsterdam we got pulled out of the line and sent off to immigration control where it took us over an hour to prove we had only been in Schengen for fewer than 90 days (it was day 89). I had anticipated the problem becasue I had read about it on line when we were there, so had copies of tickets, hotel bills etc all of which I needed so they could retroactively stamp the passport. The guy who was pulled over with us for the same thing missed the plane. So make sure they stamp you coming in. They actually retroactively stamped our passport with date of entry; they got it off by a day but I wasn't going to do anything to slow us down at that point.

I am not inclined to read all the responses you have received.
Essentially I see no link to this website http://www.seat61.com/ and more importantly the section on RailPasses starting at the bold print.