The world number one had four bogeys in his second-round 73 at Hoylake as he slipped nine shots adrift of pacesetter McIlroy at three under.
And Scott - the 2012 runner-up - knows exactly where he went wrong heading into the third day of play.
"Today was much tougher out there," Scott told reporters.
"There was just the slight direction change and the gusts -- all of a sudden there were holes where I was hitting six-irons through in the 140s.
"That's when you know it's pretty windy, and the drives are going miles and four-irons are going 300. You know it's crucial on how well you adjust to that on day like today.
"The couple of errors today were just on how strong the winds was [sic]."
Scott added: "It's the strongest wind since I've been here and then all of a sudden, on down-wind, the ball was going was going very far on the greens and downhill a bit more.
"They went 20 or 30 yards almost - some balls bouncing on the greens coming in with an iron. We just haven't seen that yet.
"That kind of got my attention after a couple of holes and I was a little bit more cautious, because I went over the back and made bogeys."
Saturday's third round is set to wreak havoc for golfers, with thunderstorms forecast during the early hours of the morning.
But Scott - tied for 15th - feels his strength of character could prove decisive if conditions change as expected.
"It seems like we're going to see it all over the weekend," he said.
"Tomorrow doesn't look great and that's alright.
"The last 36 of a major is going to be a grind and if it's tough conditions I'm certainly up for that challenge.
"I feel like I'm swinging the club really well, so the tougher it gets, the more that favours me if I keep swinging well."