Faldo said McIlroy made a "dangerous move" in changing his club manufacturer earlier this season while he believes 14-times major winner Woods can never return to golfing dominance without regaining a "go-to shot" to use in pressure situations.
Northern Irishman McIlroy, who won his second major title by a record eight shots at the US PGA Championship in August, switched his club brand last month from Titleist to Nike in a lucrative deal reported to be worth as much as $250 million over 10 years.
"Rory went from rookie of the year to world number one with the same equipment and now he's changed absolutely everything which I know, from personal grief, is dangerous," six-times major champion Faldo told Reuters.
"Once I heard the news, I tweeted it was a dangerous move. It's risky because it's all about the feel and sound of the golf ball, it's the feel and sound of the putter face, it's the feel and sound and the torque of a driver."
Faldo, a three-times Open champion who now works as the lead golf analyst on television for CBS Sports and Golf Channel, said that even very similar brands of golf clubs would feel very different to a player who had switched manufacturers.
"Factually yes, you can get really, really close but feel-wise, sound-wise, no, not even close," the 53-year-old old added while shaking his head. "You get a millisecond at impact and you've known exactly how that sounded and reacted before.
"People say, 'Oh, Rory can adapt,' but why should he be adapting at this time in his career? He might just waltz through and it's all fine. Or you may even say, 'Hey, whatever his goals were before, he may have made them a little more difficult.'
"Feel is confidence in this game. That's your feedback and that's your trust. As Rory found out pretty quickly, he announces there are 14 new clubs in his bag and after one round of golf the putter's out, because it's different."
McIlroy made an inauspicious start in his first event with Nike equipment, missing the cut at the European Tour's Abu Dhabi Championship last month when he ditched his new putter after struggling with it in the opening round.
The world number one has since taken a four-week break from competitive golf and returns to action in Wednesday's opening round of the WGC-Accenture World Match Championship at Dove Mountain where Woods, a three-times winner, is also competing.
Faldo, who was renowned for his work ethic and shrewd course management during his prime, pinpointed self-confidence as perhaps the crucial component in a champion golfer's make-up.
"You've got to have real self-belief," said the Englishman who was arguably one of the most driven players ever in his quest to reach the very top of the game.
"Whatever shot you're trying to pull off, you've got to have the belief it's going to work. And if it doesn't ... it'll start sewing those little seeds of doubt in your mind and those seeds grow and they can end up as oak trees in your head."
Woods used to intimidate his rivals with his dominant golf and immense self-belief but all that changed for Faldo after the American's spectacular fall from grace at the end of 2009 amid revelations about his extra-marital affairs.
"It's more than three years since the crash-and-burn in his personal life and I personally think he has a lot to deal with there, right from when it all happened," Faldo said.
"In golf, you have to be completely engrossed and free just to go out and practise 100 percent. There's nothing worse if you then get distracted for good reasons or bad reasons.
"If somebody is in your ear or you are worried about something ... it's much harder to have that peace of mind."
Woods clinched his 75th PGA Tour title by four shots in the Farmers Insurance Open at Torrey Pines last month but he dropped four strokes in his last five holes in blustery conditions mainly due to wayward driving.
"When he's on (form), he's fabulous ... but there are certain shots on the golf course he's struggling with and he showed us at Torrey he's still struggling with them," said Faldo.
"I don't think he has yet what we call a 'go-to shot' and you've got to have that one when literally, if someone puts a gun to your head and says, 'Right, hit me a fade,' you can aim down the left edge of the fairway and it peals back.
"If he really sorts that out, he could be unbeatable but that (doubt) may be starting to engrain itself in him."
Woods has not won a major since the 2008 U.S. Open at Torrey Pines and his burning desire to eclipse the record 18 piled up by Jack Nicklaus, in Faldo's view, will never be fulfilled.
"You can't say it's impossible but I am leaning towards no," said Faldo, whose own work ethic came straight out of the Ben Hogan manual.
"I don't think it will happen. Getting five more (majors), that's more than a really, really fantastic career (for most players).
"It's a big climb after how he has shaken himself up mentally. The biggest thing is how Tiger must look at himself in the mirror and wonder what happened. It's a lot to deal with."
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