The change in the course was immediate after heavy rain halted play for almost two hours Friday.
Stroud carded a level-par 71 while Matsuyama, who started level with Kisner, slipped back with a 73.
Matsuyama is looking to win his first major.
"Given it's the first round, I know I'm still in it, but I know that tomorrow's round becomes that much more important", Spieth said. "I feel like I have the game to compete in majors, and tons of 30th, 40th and 50th-place finishes".
Kisner, meanwhile, used his "Texas wedge" from off the green to sink a 47-foot putt at the par-five seventh - his 16th hole - and vault clear of the field, at least for a while.
On Friday, Matsuyama shot a bogey-free 64 which had seven birdies, five of which came in the last seven holes.
"I'm just excited about the opportunity".
"I'm really fired up about it the way I'm hitting the golf ball", Kisner said. Coupled with the fact that I hit the ball above the hole most of the time.
Only 17 players are under par on the tough Quail Hollow course that features length and demands accuracy off the tee to set up approaches to greens with crowned tops. "I played even par after the delay and that's not very good, in my opinion, on those holes that we had left".
Coming off his second World Golf Championships victory last week after shooting a record-tying final-day 61 at the Bridgestone Invitational, Matsuyama credited his improved putting for Friday's score. Three of the top six players on the leaderboard - Kevin Kisner, Jason Day and Francesco Molinari - made eagle on Friday, as did 54-year-old Vijay Singh. I've used a new putter too.
"I was out of it, but I gathered a little something off that Sunday round that led to two wins in two tournaments after that including a major", he said. Last week gave me an unbelievable sense of calm.
Fox's 66 was the low round of the tournament till that point, and comprised four birdies on the front nine and a further two, plus a lone bogey on the par-four 11th, on the inward nine.
After starting his round with bogeys on two of his first four holes, McGirt bounced back with a pair of birdies on Nos.
What does Spieth think he needs to shoot Saturday to get back in the mix? With the projected cut line at the time drifting between +3 and +4, it remained unclear as to whether he would survive to see the weekend.
American Rickie Fowler, hoping Quail Hollow will yield his first major championship, is next best in the clubhouse, five shots behind after a 70.
That dropped Kisner from 10-under, following birdies in his previous two holes, to eight-under and a temporary tie with Chris Stroud.