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SANTA CLARA

Sunday afternoon, the 49ers will play their third preseason game, which football coaches call “the dress rehearsal.” It’s a dry run for the regular season opener. The 49ers will treat this exhibition as if it’s a real game. Coaches will game plan for the Minnesota Vikings, starters will play the entire first half and substitutes will enter the game for specific plays in specific situations just like during the regular season.

These are five main things you should watch during the 49ers dress rehearsal against the Vikings on Sunday.

1. Substitution patterns. This Sunday, we should see exactly how the coaches plan to use their players during the regular season and whom the coaches plan to feature Week 1 against the Carolina Panthers.

On offense, we will see how the coaches plan to feature their fullback, whom they call an “offensive weapon” — Kyle Juszczyk. We’ll see how they rotate their tight ends. And we’ll see which running back will be the primary change-of-pace back — Tim Hightower, Joe Williams or Matt Breida.

On defense, we’ll see which players will play in the base defense and which will play in the Nickel and Dime defenses. We’ll see which defenders play in short-yardage situations and which play in long-yardage situations. And we’ll see if veteran linebacker NaVorro Bowman will play on passing downs, or if he’ll be a run-stopping specialist. More on Bowman below.

On special teams, we’ll see who will be the primary punt returner. We’ll see who will be the primary kick returner. And we’ll see who will be the primary “gunners” on the punting unit — the two players who line up like wide receivers and sprint down the sidelines to tackle the punt returner. The starting gunners probably will make the final roster.

2. NaVorro Bowman. On Thursday, I asked defensive coordinator Robert Saleh if he is committed to playing Bowman on third downs during the regular season, or if Bowman will platoon with third-down pass-coverage specialist Ray Ray Armstrong.

“I don’t want to close out anything,” Saleh said. “We’re going to put on the best 11 players to give us a chance matchup-wise to make sure that we’re in a position to be successful on game day.”

Notice that Saleh gave himself an out. If Bowman struggles in pass coverage, Saleh reserves the right to play someone else. Sunday will be Bowman’s first test. If he gives up a few catches, expect Saleh to platoon Bowman and Armstrong during the regular season.

3. Carlos Hyde. Through the first two preseason games, Carlos Hyde has not performed well in Kyle Shanahan’s outside-zone running scheme. Hyde has missed holes and failed to pick up yards the offensive line has created for him. He has gained just 26 yards on 10 carries.

But 20 of those rushing yards came on three of Hyde’s final four carries last week against the Denver Broncos — he had a 6-yard gain and two 7-yard gains. Granted, Hyde was rushing against second-string and third-string defenders, but he still executed the runs perfectly. He spotted the openings, made the cuts, “got skinny” as football coaches say, knifed his shoulder sideways and slithered through the holes.

Is Hyde finally comfortable in the 49ers new offense? Will he find the openings and make the cuts consistently Sunday against the Vikings? Or were those three good runs against the Broncos mere flukes?

4. Penalties. Officials have thrown 35 flags against the 49ers during the preseason. But, the continuous lack of discipline and focus isn’t an issue yet. The Niners get a pass for all their unforced errors in the first two preseason games.

If the unforced errors persist during Sunday’s dress rehearsal, then there certainly will be cause for concern. None of the substitution patterns, running back rotations or linebacker platoons will matter if the 49ers commit 17 penalties per game. They’ll be just a bad, sloppy team.

General manager John Lynch addressed the penalty problem during an interview on KNBR Thursday night. “It’s something we’ve been working on. We obviously haven’t done a good enough job yet of fixing and correcting that. I can tell you that it’s been emphasized with great focus this week and I’d be very surprised if that continues. It can’t continue. Our guys understand that.”

We don’t know how the coaches went about fixing and correcting the penalty issue this week — the 49ers closed practice to the media. Maybe the coaches benched the players who committed penalties, or made them runs laps after practice. Whatever the tactics were, Lynch believes they will work.

If they don’t work, Kyle Shanahan will need to change them, and fast. Or he’ll look pretty bad.

5. Pass concepts. Here’s an abstract concept for you to think about.

Football is not a game of plays — it’s a game of concepts. A concept, for example, is two or three routes an offense can run a lot of different ways. Each concept can include multiple plays. Every NFL team’s passing game has only about 15 major concepts. In football lingo, they’re called Smash, Yankee, Dagger, Stick, Hi-Lo, Levels, Flood, Four Verticals, Drive, Spacing, Hank, Slant/Flat & Double Slant, Mesh, Pin and Option (in a future column, I will explain what each of these is).

An offense has to work to establish these concepts, even during the preseason. And it establishes these concepts through repetition of various plays, running them during games as many times as possible. Saving or hiding certain concepts for the regular season only sets back an offense’s development.

Bill Walsh’s offenses were great primarily because they used the same few concepts all the time and perfected them. Walsh would use one concept a million different ways, with different personnel groupings, different formations, different shifts, different motions — so it seemed like he was calling a million different plays. But he really was calling the same concept with the same progressions and reads.

Two days before the 49ers’ first preseason game, a reporter asked head coach Kyle Shanahan how much of his offensive playbook he would use during the preseason. “Not much at all,” Shanahan said, noting he is “very well aware that any play that works in the preseason will not work in the regular season.”

Fair enough. Shanahan can save certain specific plays for the regular season. But he needs to feature his core concepts one way or another during the 49ers’ dress rehearsal. Needs to give his players as many chances as possible to practice these concepts at game speed before the regular season begins.

Watch how many different concepts Shanahan features Sunday against the Vikings. Will he feature a deep-passing concept? He didn’t during the first two preseason games.

The deep ball is part of the foundation Shanahan’s offense. Starting quarterback Brian Hoyer threw deep balls every day during training camp and completed most of them — he’s a good deep passer.

For the 49ers to have an effective offense during the regular season, Hoyer will have to complete deep passes. The running game is too inconsistent and the offense commits too many penalties for Hoyer to lead long, 10-play drives.

Look for Shanahan to unveil some deep-passing concepts Sunday against the Vikings. If he doesn’t, then shake your head.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for The Press Democrat’s website. You can reach him at grantcohn@gmail.com.