1) We don't think that pass will be good deal in this case - Eastern European rail travel is rather cheap and in most cases do not require a lot of must purchase in advance tickets, so it's not worth it to be strained by exact number of pass days. Pass (like East European Pass) is Ok only if you plan to do the trip fast and don't bother with purchasing tickets.
2) Concerning the route: probably 100 euro difference seems rather big, so lets look at Frankfurt...-Frankfurt route.
Krakow in your case is the most problematic destination in terms of logistics, so it's better either to start with Krakow and go Frankfurt-Krakow or to finish with Krakow and go Krakow-Frankfurt
a) Frankfurt-Krakow (from 39 euro, daytime travel, purchased online and in advance from DB website), Krakow-Prague - regular tariff is only 36 euro (+sleeper if you want), Prague-Budapest (daytime from 19 euro,
https://eshop.cd.cz/search.aspx?lang=E), Budapest-Bratislava (12 euro, purchased any time); Bratislava-Vienna (11 euro, purchased any time); Vienna-Frankfurt (daytime or overnight from 29 euro, purchased in advance from DB website)= app.150 euro for the whole trip.
b) Frankfurt-Prague (from 29 euro, in advance from DB website); Prague-Budapest (daytime from 19 euro,
https://eshop.cd.cz/search.aspx?lang=E), then the route depends on the fact either you can purchase in advance discounted ticket Budapest-Krakow (from 25 euro, needs to be purchased at least 3 days in advance at the station) or Vienna-Krakow (from 29 euro, same story - in advance). If first option, then go Prague-Vienna (from 19 euro,
https://eshop.cd.cz/search.aspx?lang=E), Vienna-Bratislava (14 euro, any time or cheaper bus), Bratislava-Budapest (12 euro). If second: Prague-Budapest (19 euro), Budapest-Bratislava (12 euro, purchased any time); Bratislava-Vienna (11 euro, purchased any time).
In case you don't want to "hunt" for discounted tickets from Budapest/Vienna to Krakow, then go Prague-Budapest (19 euro); Budapest-Vienna (from 13 euro, purchase at least 3 days in advance or 23 euro - any time), then Vienna-Bratislava (14 euro, any time or cheaper bus) and Bratislava-Krakow (app.45 euro, any time). Or you can win app. 12-13 euro if you break your ticket and purchase Bratislava-Bohumin (17euro) and Bohumin-Krakow (15 euro)
Krakow-Frankfurt starts from 50 euro on DB website (daytime option).
It's a lot of info and options, so feel free to ask further questions