However, he fears that the Holywood star could encounter more difficulty switching to his new driver.
Stockton (71), a key figure on McIlroy's back-room team since they started working together in the wake of his dramatic Sunday afternoon collapse at the 2011 Masters, wasn't worried when McIlroy controversially reverted back to his old Scotty Cameron putter after just 18 holes at last week's Abu Dhabi Championship.
Two-time Major champion Stockton, who led the US Ryder Cup team to victory in the 'War on the Shore' at Kiawah Island in 1991, maintained his reputation for straight talking in an interview with Rex Hoggard of the ' Golf Channel'.
Saying he hadn't been surprised by McIlroy's decision to leave the Method putter out of his bag on Friday in Abu Dhabi, Stockton explained: "When I texted back and forth to him, he said he was going to go the first round with it and he thought he'd be alright.
"It will just take him a while (to adjust)," added the American, who is scheduled to work with McIlroy early next month when the Holywood star returns to his Palm Beach base after a short break in the Alps with girlfriend Caroline Wozniacki.
"With his touch, Rory will have more problems with the driver. That will take him a little bit longer to get."
McIlroy's extraordinary talent was seen at its best when he wielded his old high-performance Titleist driver, and Nike's greatest challenge is to provide him with a club to complement his exceptional skills.
Meanwhile, England's Chris Wood, at 6' 5" one of the tallest players in pro golf, looked set to scale new heights and clinch his first European Tour title today after a third-round 64 put him three clear at the Qatar Masters.
Yet Wood (25), winner of last year's Thailand Open on the One-Asia Tour, must keep his foot on the throttle in Doha, judging by the equally impressive third-round 64 shot by former BMW PGA-winner Simon Khan and the resurgence this week of New Zealand's Michael Campbell as he pursues his first victory since the 2005 US Open. Sadly, the Irish challenge petered out yesterday. Damien McGrane was closest in a share of 31st on six-under after a 70, while Michael Hoey was three further back in 52nd after a lacklustre 74 that included two double-bogeys.
Six-times champion Woods eagled the par-five 18th, his ninth hole of the day, en route to a seven-under-par 65 on the easier North Course, one of two layouts hosting the fourth PGA Tour event of the season.
Qatar Masters, Live, Sky Sports 2, 8.30am
Farmers Insurance Open, Live,
Sky Sports 4, 6.0pm