1. If you’re planning on a true budget trip — staying in hostels, mostly eating from markets and street vendors, limited beer and wine and very little partying, I’d plan $75 US per day. This dos NOT include transatlantic airfare and city to city transportation. $100 per day will cover a few improvements from the bare bones travel style and $150 per day should cover “moderate tourist class” hotels (assuming 2 of you share a room) and eating every meal out.

2. A rail pass and the number of cities you visit are totally unrelated. Rail passes are sold by the day — either consecutive calendar days or “rail days” (you choose the specific days you use the pass) depending on which type of pass. Every rail pass covers an unlimited number of cities within the eurail countries or whichever countries you choose in the case of a select pass. I’m not sure why the trip planner didn’t give you a recommendation on the best rail pass for your itinerary, but try that again.

3. The cost of a 3 month consecutive day global pass should give you a good estimate of what you’ll spend on flights, trains, ferries and buses in 3 months, but, IMO, it’s unlikely to be the best option. Another rule of thumb for the city to city transportation budget is $150 US per week.

4. You might be able to get around the 90 day Schengen visa issue with two passports, but I wouldn’t try it. Your 2nd passport won’t have a stamp showing when you entered Europe which will raise issues when you leave Europe and may raise issues when you enter or leave a non-Schengen country. You should repost this question under “packing” to get more opinions.