I'm really late to this dance, but I'm going to give you the "old radio guy" take on this from both guys' perspectives:
1.) Harbaugh was a horrible guest. He was clearly not prepared for the interview, as evidenced by the way he handled the first question... if you go for the "Hi Collin, how are you," approach instead of answering the question, that's going to set the wrong tone for the interview... and then it was all downhill from there, to the point where Harbaugh was openly hostile with the "50 questions" bit at the end.
2.) Cowherd is a great radio how, HOWEVER, I'm not sure he's a great interviewer. Barbara Walters was a great interviewer, but I don't think she could carry a 3-hour daily call-in show. Two totally different beasts, and I'll say that interviewing someone live on the air was a much harder skill to master than simply talking about the news (interviewing 10-year-old 4-Hers about their county fair projects was the hardest thing I ever did on the air, and it felt like what this interview sounded like... Yes, Jim Harbaugh was essentially a 10-year-old in this example). Rush Limbaugh (remember, no politics, thank you) is another example of someone who is very good at running a long-form talk show, but is a horrible, horrible, horrible interviewer... which is why he so rarely takes calls or has guests on the show.
3.) Was it Cowherd's best interview ever? No, he was a bit harried, but I think that's because he doesn't love doing interviews all that much. But Harbaugh was the problem here; unprepared, disinterested, combative. A bad recipe for an interview any way you slice it.