I will likely get flamed for this, but I don't have a big problem with these rankings. Yes, I think Carroll is about 3 spots higher than I would put him but he has a ring. Carroll's offensive staff is arguably better than Harbaugh. Other than that, I think the top 5 is just fine.
I would put John ahead of Jim for two reasons: ring and game management including sideline demeanor.
Jim has received praise for turning this franchise around, and that is fine, however, he inherited a loaded roster that was ready to win. He can thank the terrible Nolan/Singletary years for bringing high draft picks to the team. Also, Alex Smith had already "turned the corner" before Harbaugh arrived if one looks at Smith's numbers after Singletary fired Jimmy Raye. Give Harbaugh credit for recognizing Smith was the best available alternative but as to resurrecting his career, that is an over-statement.
Harbaugh's continuing with Greg Roman as OC after three years of the same kind of play calling problems is a major issue, IMO. In fact, there has been a pretty good discussion of this in the Mike Iupati thread. Harbaugh is the head of the snake. Roman is the cause but Harbaugh is the one that approves it.
Somewhere back in the NT archives is a post I put up last year in which I ranked Jim #8. I was flamed then and will be again but that is my opinion. Go back and read what some of the more insightful 'zoners have said on the subject and you will see I am not the only one that does not perform their morning devotionals at the throne of Harbaugh. He is a good, not great coach.
Let the fires begin...