A. failed to correct it. The troubles? First of all that is incorrect since troubles is plural. Secondly it alters the intended meaning that we are trying to correct the stagnation, missteps and blunders.
B. This is a run-on sentence "so that they have failed to correct." Correct what?
C. This looks tempting, but remember, "in that" is only used for qualification. eg. Colleges can be difficult to get into, in that some of them have rigid recruitment policies. There's no cause-effect, but it provides a special case of when colleges are difficult to get into. Are we really qualifying that the troubles are a result of certain things, by saying no one could correct them?
D. Perfect. "that" correctly modifies the three causes of the troubles and says that attempts failed to correct them.
E. "Attempts at" is unidiomatic, and "correct them" is redundant and incorrect.