In every large city I've been in, there have been street markets and grocery stores - even in Eastern Europe - where you can easily get fresh fruit & veggies.  If these exist in Chicago, Paris and Moscow, I'm incredulous that they don't in Prague, etc.  

Things like fruits, nuts, power bars, vitamins, are small and can easily be carried with you.  Since you don't eat dairy or bread, I don't know what you normally eat to feel full, but if possible, bring something like that along with you.  Maybe Also try to concentrate on breakfast, which will keep you full and energized through the day, and dinner, which you probably want to sit down and enjoy, and not worry about "getting lunch on the go."  Just carry snacks with you.  And something for your stomach should you get an unfortunate surprise.  

I don't think German and Czech cuisine are radically different from each other, or even radically different that the cuisine of other parts of central Europe, comparatively speaking.  Pretty meat n' vegetables heavy.  Though, again, the cities probably offer everything from sushi to felafel.

You'll be ok, I think.  

"Pretending that you already know the answer when you don't is not actually very helpful." ~Migeru.