The 49ers have been by far the worst team in the NFL during the preseason.

In two games, the Niners have scored three points and given up 57. That means they’ve been outscored by 54. The Cowboys have been the second-worst team in the preseason. They’ve been outscored by merely 27. That means the 49ers have been twice as bad as the second-worst team.

We know the 49ers still are a quality team. We also know the roster isn’t as deep as it used to be. The 49ers have some horrible backups, like Blaine Gabbert and Jewel Hampton, who should not be on any NFL roster.

Gabbert and Hampton played a lot in the first two games, which partially explains why the Niners were so awful. The starters barely played. But the starters probably will play most of the first half and possibly part of the third quarter against the Chargers on Sunday. Joe Staley and Vernon Davis and Anquan Boldin and Eric Reid will play and we expect those four will play well.

The coaches should pay attention to four problem areas:

1. Colin Kaepernick. All offseason he worked on his weakness – accuracy, touch, going through progressions and passing in the red zone. Through two preseason games, he has shown very little improvement in those areas. To his credit, he completed a couple of passes to check-down receivers against the Broncos last Sunday.

In the past, Kaepernick had a tendency to scramble instead of throwing the check down for a couple of reasons – he’s a good scrambler and his throws lack touch. It’s not easy for him to hit the check-down receiver. Kaepernick is a former pitcher and when he throws short passes he looks like one of those pitchers who can’t make the simple throw to first base.

He still has lots to prove. Has he improved his downfield progressions? Can he look right and then throw downfield to his left?

Has Kaepernick improved his accuracy? He overthrew Brandon Lloyd deep in the end zone last Sunday.

Has Kaepernick improved his touch? He threw a pass as hard as he could at Stevie Johnson on third and 8 last Sunday. Johnson had absolutely no chance to catch the pass and it was incomplete.

Has Kaepernick improved in the red zone? He has not yet thrown a single pass in there.

2. Joe Looney. Since Jim Harbaugh became the 49ers’ head coach, the strength of the Niners’ offense has been the offensive line. It’s been the best run-blocking offensive line in football. But two-fifths of last year’s starting O-line is gone. Jonathan Goodwin signed with the Saints in the offseason and Alex Boone is holding out.

If the 49ers and Boone don’t reach an agreement on a contract extension, Looney will have to replace Boone at right guard. Boone is one of the best offensive linemen in the NFL regardless of position – he could start at left tackle for half of the teams in the league. If he had been a free agent this offseason, some team probably would have offered him a five-year contract worth about $20 million guaranteed.

If Looney had been a free agent this offseason, no team would have offered him any guaranteed money. He’s a novice. He’s played 71 snaps in his two-year career. And he’s played poorly through two preseason games this year. And he’s been particularly bad as a run blocker. Can he at the very least be serviceable?

3. Daniel Kilgore. The 49ers might be able to overcome one weak link in the offensive line if Looney is no good. In 2011, Adam Snyder was the starting right guard and he was no good – the 49ers’ offensive line still dominated. But the 49ers might have two weak links in the O-line this season. The past three years, Goodwin was the starting center and one of the best run blockers on the team. From 2011 to 2013, Pro Football Focus gave him a +38.3 run-blocking grade. Joe Staley and Mike Iupati were the only 49ers who received higher run-blocking grades from Pro Football Focus during those three seasons.

Kilgore is a novice like Looney. Kilgore has played just 114 snaps at center in his three-year career. In the past two preseason games he did not run block or pass protect very well.

4. Ahmad Brooks. Including the three playoff games last season, Brooks led the 49ers in sacks with 14. The 49ers need another season like that from Brooks. He’s the Niners’ best pass rusher other than Aldon Smith, who most likely will be suspended at least for the first four games of the season.

Smith missed five games last season and the 49ers won all of them. But they played some terrible teams – the Rams, Texans, Cardinals, Titans and Jaguars. Only the Cardinals weren’t terrible. This season, the 49ers may not have Smith when they will face some of the best offenses in football. Three of the 49ers’ first-four opponents – the Cowboys, Bears and Eagles – finished top-six in points last season.

The 49ers need Brooks at his best if Smith is out for the beginning of the season. So far Brooks has generated zero pass rush in preseason. He’s 30 years old and has played 3,469 snaps the past three seasons including the playoffs – more snaps during that period than any other player who currently starts for the Niners’ defense. Brooks has played more snaps than Patrick Willis. Is Brooks all used up?

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.