SANTA CLARA, Calif. -- It's the day after his first preseason game as an NFL general manager and John Lynch is in his office early to grade film of Friday's exhibition.

He has his grade sheet, same as a coach would, and as he breaks down the tape, what sounds like some Motown-era music plays softly in the background. The practice fields beneath his office veranda are empty for now, and while Lynch is hard at work and cognizant of the grand scale of the operation he has undertaken, there are some early rewards as well. He and rookie head coach Kyle Shanahan have overturned the roster and recast this proud NFL franchise, and consider me among those who believe they'll make some immediate strides in 2017.

Amid all of their work on talent and personnel, Lynch and Shanahan have made a habit of maintaining some time for each other, every day, at least a 15-minute window or so to make sure they are on the same page and to share candid thoughts on the process of making this club a contender again. Already the defensive line looks like it could be a definitive strength and the offense will certainly be more functional and operational than it was under Chip Kelly. I wouldn't bet against San Francisco tripling last year's win total (a 2-14 disaster) and not resembling that horrific outfit that lost 13 straight games at one point.

"You think you've done a good job," Lynch said, "but then you play your first game and you realize you've got a long way to go. We've got a thing downstairs [in the team facility] that says, 'It's not going to be easy, but it's going to be worth it.'

"So I took a look at that this morning and it reminds you, like when you are starting to lose guys to injury like everyone does. And we don't have that depth that some other teams do; we're just not there yet. But, hey, we knew this when we were signing up for a team that was 2-14, and we've got a ways to go, but there were a lot of good things."

John Lynch and Kyle Shanahan have their work cut out for them in San Francisco. USATSI

The 49ers got back to their facility around 4 a.m. after their 27-17 victory over the Chiefs at Arrowhead Stadium, and then the grind began anew. Lynch can't go long in any conversation from his office without his eye shifting back to the board at the opposite end of his desk, with the team's roster and depth charts, and his natural enthusiasm for the job shines through. It's a job he hardly had to take as a successful broadcaster with Fox with a high quality of life. Outside of his playing days, he has never served as an NFL scout, exec or employee of any sort.

What he lacks in on-the-job evaluating and GM experience, however, can be learned, and he and Shanahan are trying to make their relationship paramount, knowing that any organization is only as strong -- or vulnerable -- as that essential bond.

"I'm really enjoying it, I really am," Lynch said. "All the things that are a part of it. I've never done it before, and I've never been in this role, but there's a process we put in place and we've got really good communication. And the thing I'm most proud of is -- everyone talks about collaboration between the coaching staff and the front office -- but I think we've really done it.

"And that starts with -- and thank god I have people to rely on like Tony Dungy -- who told me the most critical thing you can do is make sure you get time with Kyle, because if you two are on the same page then the entire building will be on the same page. So we've had really good conversations challenging each other to articulate our philosophies, and fortunately it's like me and my wife -- we tend to have the same values, and Kyle and I tend to have the same line of thinking. Not always on every player but a general thought process and a lot of that comes from our background."

The ties that bind

Much is made of the fact that Lynch played for Kyle Shanahan's father, Mike, and the obvious ties that are there. But Lynch and the younger Shanahan were more like acquaintances than close friends. They were by no means a package deal as coach and GM, though they had spent hours over the years sharing ideas when Lynch would come to town to broadcast games involving Kyle Shanahan's teams, whether in Tampa, Houston, Washington, Cleveland or Atlanta.

"He didn't really like going to the production meetings," Lynch said. "So we'd talk on the phone and have really long conversations, because I was interested in what he was saying. And he stayed on the phone, so he must've been interested in what I was saying. And we realized a lot of the beliefs were the same."

Shanahan's time studying under esteemed Tampa defensive coordinator Monte Kiffin -- a mentor to Lynch from his playing days with the Bucs -- meant the two men saw defense from a similar set of eyes. And on offense, where Shanahan is among the most creative and dynamic play designers and play callers in the NFL, the reality is Lynch is shopping for the players his head coach knows fit his designs.

Lynch played the final four of his 15 NFL seasons in Denver under Mike Shanahan. Getty Images

The men want their relationship to be as up-front and transparent as possible, so during the draft prep (where the 49ers expertly worked the board and trades to come up with likely immediate impact defensive studs like Solomon Thomas and Reuben Foster), Lynch brought in one of his old professors from Stanford, who consults with many top companies.

The entire coaching and football operations staffs were brought in with the professor leading dialogues to put down on paper what core beliefs the 49ers would share in selecting players.

"He's very talented at pulling things out of you," Lynch said of the professor, and then with that mission statement crafted, everyone except the coach and GM were kicked out of the room.

"It was just Kyle and I, and we had a really deep conversation about what's going to happen in the draft," Lynch said. "And (the professor said), 'John says he has (control of) the draft, but you say you guys are going to do that together. How's that going to work, Kyle? What if it's the first pick and you don't like the guy John is taking?'"

"Those are tough questions, but it was never awkward, and never has been and we understand that it has to be a process, but we really want to collaborate and it's what we've done very well and we've continued to make the time. It's not as easy now; he's not only the head coach but he's with the offense in their meeting all the time, too. So we catch our 15 minutes here, or our 20 minutes there."

It has served them well so far.

Only place to go is up

Undoubtedly, this defensive front seven will be more menacing and robust. The defensive line should anchor this team, with some existing talent there. Thomas was a little apprehensive early in camp -- he missed the offseason due to the NFL's arcane rules regarding college classes -- but jumped out against the Chiefs.

Some teams were scared off by Foster's shoulder injury and attitude, but never the 49ers.

"It wasn't like Kyle and I were like, 'Screw the doctors, we stayed at a Holiday Inn Express last night and his shoulder is alright!" Lynch joked.

He said the 49ers medical team felt comfortable in Foster healing from a rotator cuff surgery. "Believe me, we kept going back to our doctor and saying, 'Everyone is saying there's something wrong.' And he went back and said there is no problem with his shoulder."

Elvis Dumervil, who played two seasons with Lynch in Denver, is in tremendous shape and healthy and will give the 49ers more than he gave Baltimore last year when injured. He could bookend with Thomas in obvious pass-rushing situations. If veteran linebackers Ahmad Brooks and NaVorro Bowman can hold back time some, this team will be impressive up front. The secondary, well, I'm not sold, but there was no way Lynch and Shanahan could address everything in Year 1.

Lynch rolled the dice on Reuben Foster after repeated consultations with 49ers doctors.  USATSI

Offensively, the guard situation has to sort itself out, and the interior of the line may still need work, but the 49ers are good at tackle, which ain't a bad place to start. Quarterback Brian Hoyer knows this system inside out and at one point he and Shanahan had the Browns at 7-4 and in first place in the AFC North, so that position will be a major upgrade.

Marquise Goodwin is a burner who could have a real breakout season under Shanahan, who knows how to translate speed to production at that position better than most. I bet fullback Kyle Juszczyk, signed in free agency from Baltimore, catches over 50 balls in the rare offensive scheme to allow him to flourish. Veteran receiver Pierre Garcon, another free-agent pickup, has already thrived under Shanahan before, in Washington. And the 49ers have more tight ends than they need. Teams are calling to explore trades and I suspect Garrett Celek is dealt to replenish depth at another position. The Ravens and Steelers could both use tight ends.

I'm not saying the 49ers are going to the playoffs or anything … I'm just saying this team has a chance to be far better than some might expect. And if Shanahan and Lynch can truly forge the type of long-term relationship they are working on, the turnaround here might not take all that long.