Hi, It is very hard to think she misunderstands me because she is a smart and pretty girl who has a lot of sense of humor, although she is not as clever as I thought. You can say It is very hard to think she misunderstands me ,because she is a smart girl, although she is not as clever as I thought. The problem with what you wrote is that you have a lot of other 'stuff' between these two last clauses, so their contrasting nature is a little hard to see.
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HugemoleWow good explaination. Thank you!explanation, not explaination