"You" is connected not to the stem but to the conclusive from. Thus, "kowai you desu" is correct.
"Kowakatta sou desu" is the past tense of "kowai sou desu", i.e., hearsay. "Kowasou deshita" is correct.
As for the past of "you", both "kowakatta you desu" and "kowai you deshita" can be used. The former can mean the perfect tense, so the two forms are not always interchangeable, though.