The preposition for the first sentence should be 'in'. The verb form for the second sentence should be PASSED (past simple tense). You can say either: 'I'm glad you did well in your exam.' or 'I'm glad you passed your exam.' but the meaning is not necessarily the same. You can pass an exam without necessarily doing well in it. If the person just got the minimum pass grade, it doesn't mean that they did well - they might be disappointed.

Both expressions are intended to be positive praise for success on an exam. They're meanings are slightly different, though, but interchanging them wouldn't be a sin. I, for one, would prefer to use the first one. The second one could be taken as if you weren't expecting them to pass, which might come off as rude.