By Morris Phillips

(EAST RUTHERFORD, N.J.)–49ers’ rookie Aaron Lynch had two goals, which seemed light for a guy engulfed in a Sunday afternoon maelstrom, the likes of which you solely find in the NFL.

“Play football and have fun,” Lynch said.

Lynch, the team’s first of two fifth-round picks in 2014 NFL Draft was actually the 8^th of 12 guys the 49ers selected.  All 12 remain with the team, a healthy portion on the practice squad or injured reserve.  In part due to the size of the draft haul, the 49ers were universally lauded as having the best draft this off-season.  More and more, it appears the immediate assessment has wings, due to the play of two of the 12: Lynch and linebacker Chris Borland.

The pair were a big factor in the 49ers’ superior defensive effort that masked another subpar offensive performance in the 49ers’ cardiac 16-10 win over the Giants in New Jersey.

Borland continued to look like the guy he’s replacing, Patrick Willis in his All-Pro rookie season.  The Wisconsin product has only done it for three games, unlike Willis, who was a Day 1 starter, but what a three games.  Borland had 13 tackles and two interceptions on Sunday, the second which came with a 1:09 remaining on a deflection at the 49ers’ two-yard line and the team trying to defend a potential game-winning drive by Eli Manning and the Giants.  Impressively, Borland has 48 tackles in his three-game run.

Lynch figured to play less Sunday with Aldon Smith set to return from a nine-game suspension.  Defensive coordinator Vic Fangio promoted Lynch to a situational role in Week 4 against the Eagles because he wanted someone to give the defense the quickness and big-play potential that was missing without Smith. But with Ahmad Brooks failing to meet the standard he set as a long-time starter at outside linebacker, Lynch played in Brooks’ place with Smith in his familiar spot outside opposite the rookie.

That the move happened during the game, in the second quarter, and the game ended with Brooks sitting away from his teammates without his helmet nearby, makes it a story.  Also, Brooks is one the team’s longest tenured players, and favorite of his teammates, and a first time Pro-Bowler last season.  After the game, Coach Jim Harbaugh was tight-lipped about the whole thing, which at least for the moment increased the tension.

“We have something we are working through,” Harbaugh said when asked about Brooks’ absence.  The coach then refused to elaborate.

Afterwards Brooks didn’t seem like talking either.  When told that Harbaugh said ‘Working through,” Brooks said “Yeah, working through something” too.

What couldn’t be denied was the end result worked, with Smith having a quiet debut, Lynch giving the defense pressure from both ends, and Borland playing out of his mind.  Forgotten in the mix, is Michael Wilhoite, who in his second year, is merely replacing almost NFL defensive player of the last year, NaVorro Bowman.

“The standard that Patrick Willis and NaVorro Bowman have set for inside linebacker play is at the highest level,” Harbaugh said.  “Chris Borland, Michael Wilhoite, they are playing great, with a capital G, and rising to that level.”

Complicit in the mix on Sunday was Giants’ quarterback Eli Manning who is suffering through another, turnover-riddled season that has two-time Super Bowl champion and his coach, Tom Coughlin, on the verge of being run out of town.  Manning was picked five times against the 49ers and each of the recipients, Chris Culliver, Eric Reid, Wilhoite and Borland (twice) surely got a healthy dose of reassurance that they belong in the lineup with their interceptions.

The Giants scored a touchdown on their first possession of the game, then went the rest of the way with just a third-quarter field goal to show for their frustration.  Manning admitted afterwards that the 49ers made his offense one-dimensional, a tough concession for such a decorated player.

“They weren’t giving us great looks to run the ball,” Manning said.  “We needed to throw it.  We had some good looks, they hit some plays and we just didn’t do it.”

It’s not every day two-time championship quarterbacks get thrown off their game by rookies and first-time starters like Wilhoite, Borland and Lynch.

Offensively, the 49ers struggled again.  Sunday was the sixth time the 49ers have scored once or not at all in a game this season in the second half.  This time, Michael Crabtree came to life on 48-yard catch, run and impressive broken tackle to put the team up 16-7 minutes into the second half.  That was after Colin Kaepernick and crew could only muster three field goals in the first half.  Over the final 26 minutes, the team had to hold on, a tough way to survive over any stretch of games.

After the game, the medical staffs of the 49ers as well as the Seahawks in Kansas City and the Tampa Bay Buccaneers in Atlanta were investigated in regards to alleged improprieties in the dispensing of controlled substances, primarily prescription pain killers from the medical staffs to the players.  The allegations arose in a lawsuit against the league by former players who said their team’s medical staffs routinely distributed pain killers to injured players.

Team spokesman Bob Lange said of the surprise DEA inspections that “what we were told was they are random checks of team physicians as they travel to see if anyone is transporting controlled substances across state lines.  The 49ers’ medical staff complied and the team departed the stadium as scheduled.”

Seattle lose to the Chiefs on Sunday, putting both the 49ers and Seahawks at 6-4 with two of their final six games against each other.  This season, the best two NFC teams from 2013 appear to be fighting for the No. 6 slot as things stand after 11 weeks of the season.

The 49ers host the downtrodden Redskins at Levi’s Stadium on Sunday at 1:25pm.