Peter King of NBC Sports noted that Shanahan and Lynch are choosing Jones' pro day over the one held by Ohio State's Justin Fields on the same day. 49ers assistant general manager Adam Peters is reportedly set to attend Fields' pro day on behalf of the team.
King wrote signals point to Jones being the "leader" for the No. 3 overall pick.
Alabama is holding two pro days for this draft cycle, with the first coming last week. Jones said he was frustrated with his performance as a passer during the first pro day, which came without receivers DeVonta Smith and Jaylen Waddle.
"It was a little different than a typical pro day script just because of the people we had out there," Jones told SEC Network. "We had to use two underclassmen and obviously Miller, Carl and Josh did a great job. But I feel like I could’ve thrown it better. It is what it is. I have one more pro day, got to come out and show what I got.
"I really don’t think it was as good as I probably wanted it to be. I’ll probably be pissed about it for 20 minutes, but I’ll be good after that."
Jones did prove himself to be a little better athlete than some expected, running 40-yard dashes of 4.72 and 4.68 seconds and posting a 32-inch vertical leap. His 40 time was better than that of Patrick Mahomes, who is more than shifty enough in the pocket despite not being "running" quarterback.
The 49ers traded first-round picks in 2021 (12th overall), 2022 and 2023, along with a 2021 third-rounder, to move up nine spots and almost certainly take their quarterback of the future at No. 3. Jones has faced skepticism because of his physical skills—he's not the fastest quarterback in this class, nor does he have the most accurate or strongest arm—and the fact he played with first-round talent surrounding him at Alabama.
Fields, who has a relationship with Shanahan that dates back to the Ohio State product attending the QB Collective camp, may have a leg up when it comes to familiarity. If Shanahan has seen enough based on their past work together, this may be a case of simply doing his due diligence in going to watch Jones.