Rain was Friday's major theme, which will become known as the "Troon monsoon."
First-round leader Phil Mickelson set off in the dry but was engulfed in a deluge on the back nine.
The 46-year-old says he "enjoyed the challenge" and shot two-under 69 to edge to 10 under par.
Sweden's Henrik Stenson also copped the rain but shot a remarkable 65 to close Mickelson's lead to one.
The fun-loving Swede afterwards joked that being six years younger than Mickelson will surely help at the weekend.
World No. 3 Jordan Spieth lost even more ground with a 75 that dropped him to four over, right on the cut line.
Rory McIlroy couldn't get it going either and shot level-par 71 to stay two under, tied for 15th with U.S. Open champion Dustin Johnson.
Masters champion Danny Willett carded 75 to finished level with Spieth, the man whose final-day meltdown opened the door to his Green Jacket in April.
Two-time major winner Bubba Watson also ended on four over after a 76, but at least the American made par three at the Postage Stamp eighth hole following his six Thursday.
Scottish veteran Colin Montgomerie, who grew up at Troon and came through qualifying, was another who will see the weekend by the skin of his teeth after a 75.
Welsh Ryder Cup hero Jamie Donaldson was blown inside out but finished the day level par overall following a 73, to be tied for 27th.