I tocked the ALEX Train directly to Praha.
The trip trouth CZ is:
Hamburg - Nürnberg with ICE
~10Min to get the Regionalzug to Cheb and than 20 Minutes for the SC to Praha.
You know the German Trains are on Time.
If REX 3800 Donau Moldau is on time, you will change the trains absolutely without problems (I suppose - the station is quite clear and not so big). In case of delay I think R 624 Hejtman should wait maximally 10 minutes - then I recommend you to ask the conductor. However, these regional trains from Linz to České Budějovice are usually on time :)