Singh, a 34-times winner on the PGA Tour who has not triumphed since 2008, is off to his best tournament start all season after opening with a 66.
"Doing everything good ... this is a golf course where if you are on the fairway you can attack the pins," said Singh, who could have competed in this week's Senior British Open. "I practised my putting pretty good last week so it's working out."
If Singh can clinch victory on Sunday, he would become the oldest winner in PGA Tour history, eclipsing the record held by Sam Snead, who won the 1965 Greater Greensboro Open at the age of 52 years, 10 months and eight days.
Flores was a model of consistency, firing a second successive 66 in a bogey-free round which boasted an eagle on the par-five second and three consecutive birdies from the 16th to the 18th.
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American Gary Woodland soared up the leaderboard with a 10-birdie round of 63, the day's lowest, to vault into second alongside compatriots Matt Every (68) and Brandon Hagy (68).
Having started two strokes adrift, world number one Dustin Johnson shot a 69 to lie four off the pace.
Kuchar (68), who battled dizzy spells in the first round, did well to offset a back-nine double-bogey with an eagle at the par-five 13th but still needed some magic to stick around for the weekend.
The 39-year-old American caught fire with birdies at the final three holes to reach a five-under total of 139, one shot inside the cut-line.
After opening brightly with a 66, twice U.S. Masters winner Bubba Watson shot a forgettable 73 to tumble down the leaderboard into T46, level with Kuchar.
Defending champion Jhonattan Vegas of Venezuela, who started one shot back of the leaders, shot 69 to be three behind Flores.
Graham DeLaet and Mackenzie Hughes, both at eight-under and in a share of 14th place, remain in the hunt to become Canada's first homegrown champion since Pat Fletcher in 1954.
(Reporting by Frank Pingue in Toronto; Editing by Ian Ransom)
