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After visiting Krakow, the High Tatras in Slovakia, Budapest & Ljubljana, we need to get up to London. We have choices to make:
1) See more of Slovakia and work our way back to Poland by train for a flight from Krakow (not booked yet and we need to work out feasibility/cost of fitting it in with our international flights). This would be a reverse of one of your suggestions in my previous post.
2) Take a train route that allows us to stop off a couple of times in places we haven't visited before or are happy to revisit - Salzburg, Munich, Cologne, Strasbourg seems to be on the main routes.  This is probably our preferred option if we can stop over and the price is right, or even better...
3) Wait to see what alternatives you come up with   
Thank you!!

1) See more of Slovakia and work our way back to Poland by train for a flight from Krakow (not booked yet and we need to work out feasibility/cost of fitting it in with our international flights).

To be honest, it's a bit weird to come back to Poland in order to fly to UK. Obviously there are plenty of things to see in Slovenia-Hungary-Slovakia, but perhaps it might make sense to look at other options (e.g. see below)

2) Take a train route that allows us to stop off a couple of times in places we haven't visited before or are happy to revisit - Salzburg, Munich, Cologne, Strasbourg seems to be on the main routes.

It's not a problem to travel (mostly) by land rather cheaply here, for instance:
Ljubljana to Salzburg: it's possible to get discounted promo fares tickets from Villach (first big station next to Slovenia/Austria border) to Salzburg for only 9 euro, while leg from Ljubljana to Villach is just 12 euro no matter when you purchase ticket.
Salzburg to Munich: very easy and cheap, especially if traveling not alone - so called Bavaria Ticket can be bought and is valid from Salzburg, plus it allows travel during the entire day, so for the same money it's possible to turn Salzburg-Munich into whole day excursion around Bavaria (e.g. leave Salzburg in the morning, arrive to Munich & leave your thing in hotel/luggage storage and spend rest of the for the trip to the mountains, lake Constance etc.)     
Munich to Cologne: multiple options here: a) you can fly; b) travel by high-speed train (plenty of departures + discounted tickets, which can be bought from German Railways website) and c) don't bother with in advance ticket purchase and simply use slower trains & Quer-durchs-Land-Ticket/Happy Weekend Ticket (more about these tickets on our Germany page - http://europetrainsguide.com/Countries/Germany/Germany-DB.html )
Cologne to Strasbourg: again to avoid international tickets and in advance ticket purchase you can opt for Quer-durchs-Land-Ticket/Happy Weekend Ticket from Cologne to Kehl (which is small town just across the Rhein from Strasbourg). From Kehl to Strasbourg it's very easy by local transport
Strasbourg to London: again few option here: a) simply check flights from the nearby French and German airports or b) travel via Paris with high-speed TGV and then EuroStar trains (discounted tickets for both legs (from 25 euro & 51 euro respectively) available via French Railways website

3) Wait to see what alternatives you come up with 

Perhaps first thing I thought here was spending few days at the Adriatic cost (Croatian Istria, Koper, Trieste) and/or touring northern Italy (Udine, Venice, Verona, Milan etc.) with the idea afterward to fly to London from Pula/Rijeka or one of the Italian airports (all those are served by low-cost airlines, so it can be very cheap compared to by land travel option). In September it's still very warm there + less touristy, so it can be perfect ending for the European trip.

Salzburg to Munich: very easy and cheap, especially if traveling not alone - so called Bavaria Ticket can be bought and is valid from Salzburg, plus it allows travel during the entire day, so for the same money it's possible to turn Salzburg-Munich into whole day excursion around Bavaria (e.g. leave Salzburg in the morning, arrive to Munich & leave your thing in hotel/luggage storage and spend rest of the for the trip to the mountains, lake Constance etc.)     

Or opposite, if excursion around whole Bavaria is not needed - it's worth to mention there is cheaper ticket, with conditions of usage similar to Bayern-Ticket, but smaller validitiy area - not whole Bavaria, but only on a smaller part of it (but including section Salzburg - Munich).
I'ts Südostbayern-ticket, here is validity area:
http://www.suedostbayernbahn.de/so_bayern/view/wir/streckenkarte.shtml
ticket costs 17 EUR (instead 23 EUR for Bayern-Ticket) for 1 person, the similar to Bayern-Ticket each additional person is +5 EUR to price.
But important note - despite validity are of Südostbayern-ticket reaches Munich, but it's not valid for MVV (like Bayern-Ticket is).
 

Just a humble suggestion for the return trip from Munich to London.
Please consider London Spezial from Deutsche Bahn which can be bought in advance for 59 euro (Munich -> St Pancras all inclusive with Eurostar tunnel crossing)

It allows for two stopovers for up two 48 hours each - so you can visit Cologne, Nuremberg, Frankfurt or even Brussels.

BTW As a long time lurker on the forum - Thank you tUt for your amazing work.. Your knowledge and willingness to help is extraordinary!

Just a humble suggestion for the return trip from Munich to London.
Please consider London Spezial from Deutsche Bahn which can be bought in advance for 59 euro (Munich -> St Pancras all inclusive with Eurostar tunnel crossing)

It allows for two stopovers for up two 48 hours each - so you can visit Cologne, Nuremberg, Frankfurt or even Brussels.

Good suggestion. And even if two stopovers (or their timing) isn't enough, then it's possible to combine London Spezial discounted ticket with something else (e.g. first Munich to Strasbourg, then comeback to Germany (--> relatively close Karlsruhe or even Stuttgart) and use London Spezial from there, thus at the end having another two stopovers still possible