What happens at running back?
First and foremost, the Niners need to decide how many running backs they'll keep. Behind starter Carlos Hyde, they have Tim Hightower, Joe Williams, Matt Breida, Raheem Mostert and Kapri Bibbs. From that group, only Bibbs looked like a full-fledged long shot entering the preseason finale. Breida looks like he's earned a job and could even be No. 2 on the depth chart when the season gets going. Williams has lagged behind a bit in terms of playing time, but given how highly the Niners thought of him in the draft, he's likely to stick as he develops.
The real battle here might be between Hightower and Mostert. Hightower is the experienced veteran who knows the offense and would provide some stability to the group. Mostert, meanwhile, offers more value on special teams and his strong performance against the Vikings in the third preseason game put him squarely into the mix.
Coach Kyle Shanahan said Hightower would play a lot against the Chargers and he did, finishing with 21 yards on eight carries with a touchdown. Williams also got plenty of work while Hyde and Breida did not play.
Things seem to be trending toward a group consisting of Hyde, Breida, Williams and Mostert at running back but that's another tough decision that the Niners must make in the next couple of days.
How does tight end shake out?
The Niners added some clarity to this position battle Tuesday when they traded Vance McDonald to Pittsburgh, but there was still some jockeying for position that needed to take place. Rookie George Kittle is essentially a sure thing and wasn't even in uniform on Thursday night. Surprisingly, Garrett Celek also was not in uniform, and though the McDonald trade seemed to put Celek in a good spot, he might be even better off than initially thought.
From there, the 49ers had Logan Paulsen, Blake Bell and Cole Hikutini available against the Chargers. Fullback Kyle Juszczyk can also play tight end, which means the Niners probably don't need to keep more than three tight ends and could go with just two plus Juszczyk. If they do go with a third, there's much to consider among Celek, Paulsen, Bell and Hikutini.
Celek is the most established and is a good blocker. Paulsen has a similar track record and is the most familiar with Shanahan's offense. Bell has been around as well and is more of a "move" tight end, similar to Kittle. He's also been one of the Niners' most active special-teams players. Hikutini has some upside but hasn't done much on special teams and might be a better candidate for the practice squad.
The questions now seem to be whether the Niners keep two or three tight ends and who will join Kittle on the roster?
Who handles key special-teams roles?
The 49ers' special teams have struggled during the preseason, as they have racked up penalties and given up some big returns. In fairness, many players who won't make the team have contributed to both of those issues.
Still, it's something Shanahan would like to get squared away and, more importantly, the Niners would like to identify some key special-teams contributors. Among those who are flying under the radar but were worth watching entering Thursday night were safeties Don Jones and Vinnie Sunseri, defensive back Adrian Colbert and Mostert, in addition to the tight ends mentioned above.
Jones continued to make his case for a roster spot from his position as a gunner, forcing a fumble on a punt return. Jones suffered a knee injury but returned to the game. Jones and Sunseri are likely competing for one spot.
Elsewhere, receiver Victor Bolden Jr. added to his resume with a 92-yard punt return for a touchdown. Two weeks ago, Bolden returned a kickoff 104 yards for a score. It's far from a guarantee Bolden will make the roster considering his returns came against backups, but he offers a more explosive element than other returners like Mostert, Trent Taylor and Jeremy Kerley. If nothing else, Bolden has given the Niners something else to think about as they shape the 53-man roster.
“Just returning two (kicks for score) isn’t just enough," Shanahan said. "It’s got to be everything else that you do. I know they were two real good plays. But, it has to do with everything else also. How much can he help us out at receiver? Is he the punt returner? Is he the kick returner? What else can he do if he isn’t? And again, what does the 53 look like?”