Elaine Thompson/AP file photoThe 49ers and head coach Jim Harbaugh are expected to part ways when their disappointing 2014 season finishes in two weeks.

It’s a guessing game at where Harbaugh will go next

Now, the only thing left to discuss about the 49ers is where Jim Harbaugh will be coaching next season.

I don’t believe Harbaugh’s problems this year had anything to do with the front office. He and general manager Trent Baalke are both very strong-minded men but they’ve worked together in the past. There was no reason they couldn’t have done the same this year, if that’s what Harbaugh wanted.

Remember that Jed York wanted to give Harbaugh a contract extension and raise before this season started. It was Harbaugh who wanted to wait. Perhaps he saw what I saw when I predicted before the start of the season that the Niners wouldn’t make the playoffs: That free-agency losses and injuries to star defenders like NaVorro Bowman, plus the nine-game suspension of Aldon Smith, would be fatal to the Niners’ chances. Perhaps he just loses interest after reviving a program and taking it to the top, or just below.

At any rate, he’s going to be moving on. The 49ers will have to facilitate that by trading him to a team he wants to coach. Miami would be a logical destination. Stephen Ross, who owns 50 percent of the Dolphins, had an interview scheduled right after Stanford won the Orange Bowl, but Harbaugh waved that off and signed with the 49ers.

He isn’t going back to his alma mater, Michigan, though so many media people have put that idea out there forever. Harbaugh called his school out for its two-track system for athletes — which I reported in a San Francisco Examiner column — and at least temporarily alienated the Michigan people. Their attitude might have softened, but they haven’t changed the system that bothered him. He wouldn’t overlook that just to go back to his alma mater.

Colin Kaepernick will be the player most affected by Harbaugh’s departure. There is no doubt that Harbaugh targeted Kaepernick in the 2011 draft and persuaded Baalke to make a trade to move up and get him early in the second round.

Harbaugh was convinced he could make a quarterback out of Kaepernick and got him into the lineup when Alex Smith made the mistake of suffering a concussion. Smith had to miss one game and, when he was able to return, learned that he had become the backup.

Kaepernick was a sensation that season because defensive coaches had no idea how to stop him. But in the NFL, coaches look at videos over and over and over until they figure it out. It’s been obvious that defensive coaches now know how to stop Kaepernick and those with good enough players have done it this season. After a very successful run in high school and college, Kaepernick doesn’t know how to deal with this.

Bet on this: The Harbaugh-less 49ers will draft a quarterback in the first round. The college game has become an offensive extravaganza, producing many potential NFL quarterbacks. The Raiders got Derek Carr in the second round in this year’s draft. Baalke will find a good one next spring with the Niners’ first-round pick.

Harbaugh did a great job in turning around the 49ers but for both parties, it’s time to move on.

Glenn Dickey has been covering Bay Area sports since 1963 and also writes on www.GlennDickey.com. Email him at glenndickey36@gmail.com.

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