Kawakami: The 49ers' roster jigsaw puzzle — all these injuries, all these decisions

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For the last two ominous summers, the 49ers have been the reverse-hydras: Almost every time they get a player back, they lose two more.

This is not how anybody wants to prepare for an NFL season, of course. Thanks to the energy of all their new young players, the overall mood of the team appears to be much better than last year's dark-cloud environment, as Kyle Shanahan noted again Tuesday. But the fragile physical state is very familiar.

"We haven't even been able to have the training camp that we normally want to have because of the injuries," Shanahan said

On Tuesday, after two off days, the 49ers weren't initially planning on a long workout, but it was shortened even more due to the lack of healthy bodies. Isaac Guerendo and Renardo Green were two notable practice returnees, but Mac Jones popped up with a short-term knee injury from Saturday's game and Mykel Williams and Upton Stout, two players the 49ers very much hoped to see back this week, remained out.

That isn't the full list of injuries. That is barely the start of it.

And it all contributes to the massive jigsaw puzzle that Shanahan and John Lynch are dealing with right now, with Tuesday's cutdown to 53 players looming and key injuries complicating the decisions for almost every position group.

On the defensive line, Williams, CJ West, and Yetur Gross-Matos are all expected to play large regular-season roles, but none are guaranteed to be healthy for Week 1 in Seattle.

Possible tough call: Gross-Matos, a rare veteran DL holdover from last season, would be very valuable on such an inexperienced line. But with the 49ers needing to save space for younger, healthier bodies, Shanahan hinted that Gross-Matos could be headed to the Physically Unable to Perform list and therefore miss at least the first four games.

On the offensive line, Puni's knee injury will take him out for at least the first few games, so the 49ers have to figure out who takes his place at right guard (rookie Connor Colby seems to be the frontrunner) while also worrying about starting left guard Ben Bartch, who is also out for now. Which seems to be pointing to Nick Zakelj at that spot.

Possible tough call: Can the 49ers carry both Puni and Bartch on the 53-man roster — which could lead to a very thin guard group in Weeks 1-2 — or do they have to put at least one of them on IR for the first month and ride with Colby or Zakelj?

At running back, the 49ers just put incumbent RB3 Patrick Taylor Jr. on season-ending IR; rookies Jordan James or Corey Kiner would be natural replacements, but James is still out with a dislocated finger and Kiner went out Saturday with a sprained ankle. Guerendo is RB2, but he's just back. Christian McCaffrey is fine, but he's coming back from an injury-ruined season.

Possible tough call: Old friend Jeff Wilson Jr. could make the 53 as necessary insurance, which would take a roster spot from another position.

At quarterback, Shanahan said that Jones should be fine for Week 1, but the 49ers brought back Nate Sudfeld on Tuesday just in case.

Possible tough call: If Jones is a question mark as Brock Purdy's backup going into Week 1, Sudfeld could be another spot-stealer. The 49ers can cover some of this with their practice-squad signees, but the roster math could be getting fairly perilous.

Which leads us to ...

The wide receiver group is in some question, to say the least. The 49ers will put Brandon Aiyuk on IR to start the season to continue rehabbing his knee and they'll hope he's back around Week 6. Rookie Jordan Watkins' ankle injury likely will sideline him through the first few weeks of the season. That leaves Ricky Pearsall, who had hamstring issues early in camp but has excelled lately, as by far the leading healthy WR on the team.

Possible tough call: The 49ers' patience with Jauan Jennings might be nearing an end. They need him out there, at least until Aiyuk is back. If they don't have Jennings, who's getting snaps in Seattle alongside Pearsall? Jacob Cowing and Russell Gage? Whew.

Shanahan has been clear that Jennings' calf injury is real. But it's also quite possible that Jennings' contractual issue also is involved — that Shanahan and Lynch are giving Jennings some wiggle room on practicing when he has a borderline injury. But the wiggle room will probably disappear soon.

These are different situations, but last year, Lynch held a news conference to say that Aiyuk needed to end his "hold-in" as the 49ers were finalizing their cutdown decisions — and a deal was struck very quickly after that.

When I asked Shanahan on Tuesday if he's sure that Jennings is good to go for Week 1, his reply was telling, if you know how the 49ers think about these situations.

“Any player, not just Jauan or anyone, but people need to practice," Shanahan said. "They need to get ready to play an NFL season or you end up getting hurt. So, hopefully he can get his health back so he can get that out there and start practicing. Just running routes, doing things like that."

Practically, the 49ers need to know what they have at WR for Week 1 and who they can count on as they cut to 53. They have so many other positions that could use an extra player or two and they don't want to have to carry an extra WR just in case Jennings remains on the sideline.

Everybody has a theory about the 49ers' terrible injury luck in recent years — and through the entire Shanahan era, really.

And Shanahan clearly has heard the theory most often and most loudly offered by 49ers fans: That the 49ers practice too hard, which leads to most of these ligament and muscle injuries.

"It’s not like they just all happened one week," Shanahan said. "They happened pretty early with the number of guys and just the way our schedule's gone with our scrimmages, having these games, the off days and traveling, I don't feel like we've had enough of the training camp practice to say that we're going too hard.

"But obviously we have too many guys down. So we’ve got to look into all that stuff and figure out whatever we can do better.”

Interestingly, Shanahan certainly wasn't rejecting the theory outright. I don't think he believes that the 49ers' practice physicality is producing these injuries, but until they come to a better conclusion, well, it's a theory.

But I don't subscribe to it. The 49ers are at the higher end of practice aggressiveness, but it's not like their workouts are outrageous. Compared to 10 or 15 years ago, they're mostly pretty tame, actually. Compared to other teams I've watched, the 49ers' practices are very much in the same range.

My personal theory, while also noting that most injuries in this violent game are pretty random, is that the 49ers of this era have been a little too eager to add players with recent injury histories and a little too dismissive of some veterans who aren't flashy but also habitually stay healthier than most.

But it's impossible to avoid injury waves altogether. You could do everything perfectly and still limp through camp and barely get to the regular season with 53 healthy players. The 49ers have not done everything perfectly. But they've got plenty of experience with these kinds of injury/roster puzzles, so at least they've got that going for them.