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I did this exact trip back in April. I would say two weeks might be a little long for the entire trip. I did it in 9 days (3 in each city) and by the end we were getting very tired. Obviously you would want to do the cities in order working from either north to south or in reverse.
Of the three Prague was by far my favorite, but that might have been influenced by the order I visited in. By the time I reached Budapest I was eager to return to London. I would recommend starting in Budapest then and saving Prague for the end. As for a good guide, I would recommend the books by Rick Steves. I am not sure if he has one for Budapest but I know there are ones for Prague and Vienna.
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