By Nick Shook
NFL.com
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Much of the 49ers‘ quick fall from grace came as a result of internal conflict.

First, there was Jim Harbaugh versus Trent Baalke. Then there was Chip Kelly versus Trent Baalke. (Jim Tomsula was wedged in between there for a single ill-fated season, but his problem wasn’t strife within the building.)

It seems like Jed York finally might be learning from past mistakes.

New Niners general manager John Lynch and head coach Kyle Shanahan told reporters Thursday that the hiring process itself was intended to avoid such friction between two powerful men set to join forces.

“To have an opportunity where an owner gives you a chance to come in with the GM and to make sure that we both meet together before they do it, that’s what made it so special,” Shanahan said Thursday. “You don’t get that opportunity much in our business and it’s something that I never really thought I would get that opportunity. In seeing that you had an owner who understood how important that was and gave us that opportunity, I didn’t think that was something I could pass up.”

Shanahan will have control of the active, 53-man roster, while Lynch will have control of the full 90-man roster, and free agency and the draft. Even then, though, decisions will come with a requirement of the approval of the other.

“Free agency and draft, I think I have, but in all of those it’s also written that subject to approval of the other guy,” Lynch said. “That’s the way we wanted it, that’s the way we wanted it reflected, but that’s the reality of it.”

So, that seals it. Peace and love is ahead for the Niners as they attempt to rebuild a roster that is lacking in talent and have decisions to make about multiple positions, including quarterback.

Ah, yes, quarterback. About that:

“Colin (Kaepernick) reached out and we plan on visiting,” Lynch said. “That’s something Kyle and I committed to. Kyle spoke to that in order to find out what you need, you have to first really take inventory of what you have. We are still very much in the process of still doing that. We are just at the beginning of it.”

The Kapernick situation is a unique one. The quarterback went from losing the starting job after struggling with arm fatigue, to replacing Blaine Gabbert permanently as the Niners became irrelevant while trudging to a 2-14 finish. Kaepernick showed glimpses — a comeback win over the Rams late in the season was one — that he might have enough to stick around in San Francisco. But before that decision is made, Shanahan needs to look at the film.

“With me, I see a lot better than I hear,” Shanahan said. “I need to go watch it on tape. Colin, just like any other player, someone I’m going to be watching a lot of tape on over these next few weeks. Before we can look at anything, free agency, draft, anything, you have to know what the players on your team are. That doesn’t happen from just turning on a game. That happens from watching a lot of stuff. It takes a lot of time. It is a process.”

Quarterback has to be at the top of the list of decisions to make in San Francisco. It’s likely they’ll know rather soon which direction the Niners want to go at the position. And according to what the new dynamic duo of San Francisco said Thursday, it’ll be the first of many joint decisions made in the Bay.