Ok, so if you already decided not to involve overpriced pass, then let's go step by step throughout your itinerary:
Prague-Munich: here cheapest option for few passengers traveling together is Bavaria-Bohemia ticket. It's a regional pass for Bavaria and neighboring Czech regions sold by German rail. But you can as well buy in Prague. It cost 34 EUR for up to 5 passengers and valid from Plzen and further to Bavaria, works for direct trains Prague-Plzen-Munich. For Plzen-Prague leg you just purchase domestic Czech ticket - 222 CZK for two (or 216 CZK if purchased online from CD eShop -
https://www.cd.cz/eshop/). You don't even need to get off train in Plzen, just buy domestic ticket for the same Prague-Plzen-Munich train, till Plzen you'll have domestic tickets, while from Plzen to Munich - Bavaria-Bohemia ticket. You can read recent report on similar journey the opposite way -
http://europetrainsguide.com/forum/index.php/topic,78.msg1288.html#msg1288.
In case you want to do Prague-C.Krumlov-Munich, then you also can use Bavaria-Bohemia ticket for Krumlov-Munich part (here you can find map of the region/station where such ticket is valid -
http://www.bahn.de/regional/view/mdb/regio_oberbayern/2011_relaunch/MDB87054-bayern_boehmen_ticket_2011.pdf). Till Krumlov just buy domestic Prague-Krumlov ticket - 376 CZK (365 CZK with eTicket) for both. Or you can also use bus here.
Muinich-Budapest: here probably is the only connection it's better to prepurchase your ticket in advance, thus catching discounted offer. You can do it online from German rail website -
http://reiseauskunft.bahn.de/bin/query.exe/en . NB: read carefully rules of the offer, so you can avoid any surprises while traveling.
Budapest-Krakow: here you can have two options: a) cheap and simple - buy discounted (from 29 EUR) ticket from Hungarian rail website in advance -
http://elvira.mav-start.hu/elvira.dll/xslms/ , sale system isn't very efficient, but manageable. You can buy them from the ticket counter, but since tickets under such offer are limited and sold at least 3 days in advance, then chance to buy them already in Budapest are minimal, that is why it's better to buy them online now; b) since all the direct carriages from Budapest to Krakow go via Czech Republic and while coming back from Krakow to Kutna Hora you will travel the same route, then it might make sense to use special Czech Republic-Poland return discount and at the same time not to deal with purchasing Budapest-Krakow ticket in advance. The trick is that you will need to buy in Prague (while first time before traveling to Munich) two separate tickets: return Bohumin-Krakow (20 EUR per person, valid for one month) and one way Sturovo-Bohumin (25 EUR), here note to the cashier the date of your travel from Budapest to Krakow. Then in Budapest just purchase Budapest-Sturovo ticket (6 EUR) also for a date you plan to travel. Such combination of tickets will exactly cover the whole route Budapest-Sturovo-Breclav-Bohumin-Zebrzydowice-Krakow and allow you not to hunt for any offers from Hungarian rail website.
Krakow-Kutna Hora: here you can use either already mentioned in previous post full standard ticket (app. 35 EUR) or mentioned above return part of your Bohumin-Krakow ticket. For Bohumin-Kutna Hora leg just buy Czech domestic ticket - 580 CZK for two (or 563 CZK if bought from CD eShop).
Kutna Hora-Prague: that is the easiest leg, just purchase domestic ticket - either online 142 CZK or at the station - 146 CZK, both fare for two passengers.
All the above is a bit a lot of info, thus just try to read it attentively, check yourself all the things mentioned, look at links etc. If still something is not clear - we are ready to answer any follow up questions.