That made sense is the corresponding declarative sentence to the first sentence. In its assertive predicate there is no operator, no finite auxiliary. To form the negative, a dummy do support is required, which, similarly to modal auxiliaries, is to be followed by a bare infinitive form. '(M)ade' is not a bare infinitive form, but a past tense form. '(M)ake' is correct. Thus, the first sentence is ungrammatical.
You still haven't told me(,) how long (did) it took you(?).
Never place a comma between the verb and its direct object. The verb in the subordinate nominal relative clause does not require a do support because it sits in an indirect question.
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