Even the manager admitted it in his post-match interview.
"I thought we were going to get a tanking," he said to me when summing up the opening 20 minutes of a game which started on a low and ended on a massive high.
After recent games, Monday's draw with Hereford in particular, the team selection was brought into sharp focus, and when the sheet was put in front of me our tactical set-up wasn't immediately clear.
Sido Jombati was back - but Keith Lowe was still in the side.
Marlon Pack and Jermaine McGlashan on the bench, Chris Zebroski back in along with Russ Penn.
So, was it 4-2-3-1 as usual with Sido wide right and Zebs on the left?
Or three centre halves to combat Adebayo Akinfenwa, with Sido and Billy Jones providing the width as wing-backs? That would have been a risk - a formation I cannot recall us ever playing under Yatesy.
As it turned out, it was flat back four, with Keith about five yards in front of them, with Russ, Jake Taylor and Darren Carter as the middle trio and two up front, Zebs and Shaun Harrad.
Yes, two up front...
My assumption was that Pack and McGlashan were left out with an eye on Tuesday's Cup replay as they have four bookings each - but Yatesy said afterwards he would always have played that formation. Hmm. Maybe.
But saying the system didn't work at first was an understatement.
The scoreboard clock had barely ticked round a minute when Emyr Huws was allowed to get down the left side of the box and pulled back for Bayo to score all too easily.
It was rather similar to the Hereford goal on Monday, when Ryan Bowman was allowed to make a similar run and provide a similar cross before Josh O'Keefe's equaliser.
Yatesy mentioned two things in pre-match interview as the things to look out for - Bayo was one, and long throws were the second - 13 minutes in we found out why.
Ben Tozer launched a bomb in, Scott Brown couldn't get through the melee to grab it, it skimmed off Alan Bennet's head, hit Billy on the leg and bounced in.
Two down, and we were a bit of a shambles, to be honest.
The new formation was not working, Bayo was winning everything, Hackett and Demontagnac were cauting problems, we were second best in midfield and our front two were making no impression.
Lewis Hornby nearly scored from 50 yards with an effort which nearly caught Browny off guard, and he had to backpedal to claw it out. That would have put the tin hat on the opening spell.
With great honesty, the manager admitted he thought he had picked the wrong team, and was asking Neil his view on possible changes. It was that bad.
But we weathered that early storm, and to our credit didn't cave in completely as we could have done, and have done in some previous away games.
The catalyst for me was Zebroski, who started working the line well and giving Clarke Carlisle and Kelvin Langmead more to think about, while at the other end we got to grips with Bayo and kept him quiet for the last 20 minutes of the first half.
Our first goal was similar to theirs, Zebs showed great energy to burst down the left, beat a couple of players and cut back for Carter, who had made a god run himself to apply the finish.
Carter has come in for a lot of flak lately, along with Pack, but looked a lot happier in a more advanced role and was able to have a big influence on the game.
Post-match he said to me that he loves that role, and has played it for most of his career, so let's hope he stays in that role if it means we will get the best out of him.
Two minutes later we were level and it was another delivery from Billy - great free-kick, and a super header from Zebs, glancing in off the post.
For the rest of the half, we were the better side. We looked to have better energy, kept the ball better, defended the long-throw bombs better and kept Bayo out of the game.
But it was no surprise to see Northampton come out firing after the break, and once again we had to dig in.
We didn't have many chances - Harrad had one which he put wide, and a cross from Sido flashed through the box
Most of the half was spent defending long balls and more bombs into the box.
We had a bit of luck - Bayo hit the bar, Browny made a good save and Ben Harding missed a very good chance, but we came up with a bit of class to win it.
Carter started it by winning the ball and then producing a superb pass for Darryl Duffy, and it was a great finish, off the shoulder of the defender and arrowing it into the corner.
That was his first goal since March in the League, but his fifth in three games against Northampton. Can we play you every week...
Coming as it did days after he revealed he has had three loan requests turned down by Yatesy, it just adds another sub plot to the question of who plays up front for us.
Taking in the Barnet, Hereford and Northampton games, all four of our strikers have scored a goal each.
Darryl's celebration afterwards maybe summed up his mood - subdued, but maybe happy inside to have made a point to the gaffer - but as he admitted himself after the game he is not suited to the lone forward role Yatesy wants to employ in the 4-2-3-1.
Getting physical with centre-halves is not his game, but get him in the channels, running off the shoulder of defenders on to passes like Carter's and he can be deadly.
Arguably though, he might not have even been on the pitch had Jeff Goulding been fit to travel, as Yatesy has susally used Jeff ahead of Darryl...
But in the system we played on Saturday, a 4-1-3-2 becoming a diamond, maybe playing off Zebroski or Goulding, I am sure Darryl would be effective. Not sure him and Harrad would work, as they are too similar.
If it is two up front, it has to be one of Zeb and Jeff with one of Darryl and Shaun.
Yatesy will be delighted to see the strikers all scoring, and it only gives him even more options, as does the sight of his midfield yesterday showing such good energy and creativity, without Marlon and Jermaine.
I thought Jake Taylor looked happier on the left hand side and he was, as he has been in the last two games, neat and tidy, while Russ gave us what we knew we would get, competitiveness and the ability to get up and down the pitch between the two boxes.
Carter just looked happier - able to affect the game more, as he could leave the tackling to Keith and Russ and concentrate on making us more potent in the final third. Scoring one and making one and almost putting another cross on Harrad's toe just before half-time showed he did just that.
So, despite the start of the game, a great result, made even more important as the League Two fixture list this weekend showed many of the top half playing, and therefore taking points off each other.
It opens up our three-point gap on fourth place, and brings us a point behind Port Vale in second ahead of the game with them on Saturday.
But first, to Tuesday, and the small matter of that £200,000 match up the road at Edgar Street.
After 20 minutes, it looked as if we were going to go there on the back of a third hiding away from home, and needing to pick ourselves off the floor.
But now the opposite is the case. We go there confident, with the spring back in our step, and the manager has plenty of questions to ponder.
The changes and substitutions had the desired effect as some players took their chance, and showed they can be effective in different roles. They also showed some much-needed backbone.
Do Marlon and Jermaine come back in? Does Keith stay in his enforcer role? Does Darren play more advanced again? Is there a place for Mo on the left? One up front, or two? Does Darryl get a start...
My preference would be to play the same system as we did yesterday, and only make one change, Marlon for Keith Lowe.
He could play as the deep midfielder, and try to run the game, it would keep Darren further up the field, and leave Russ and Jake to nominally provide the width - but with Sido and Billy able to push up and support them.
We need Russ in there to combat Harry Pell, and I would fancy Sido to come out on top in a battle with Sam Clucas
I would also keep the two up front, and I think Zebs and Shaun put in a great shift on Saturday after a slow start and deserve the chance to keep their partnership going.
So my team would be (4-1-3-2): Brown, Jombati, Bennett, Elliott, Jones; Pack; Penn, Carter, Taylor; Zebroski, Harrad.