Further downpours on Saturday prompted officials to cancel play for the entire day as they worked to get the course, particularly the flooded bunkers, in shape.
Showers punctuated Sunday's play, and the third round finally got under way in steady rain shortly before 3:00 pm (2300 GMT) that intensified until organisers called a halt after 30 minutes. About two hours later the round was halted for the day, and set to resume at 7:30 Monday morning (1500 GMT).
Scott had five birdies in his five-under effort. Four of them came on Sunday, including back-to-back birdies at 16 and 17 and a birdie at his final hole, the ninth.
A dismal weather forecast prompted fears that not even three rounds could be completed, even if the tournament was stretched into extra days.
Tournament director Mark Russell said organisers would do all in their power to complete at least 54 holes, and he didn't rule out the chance of 72 if the rains passed through and left sunny skies in their wake.
The last time a PGA event went only 36 holes was the 1996 Buick Challenge, which was won by Michael Bradley in a five-way playoff.
Amid the uncertainty, several players said they started the day Sunday on the assumption that 36 holes would be all they had.
Clarke was joined on 134 by first-round leader Brian Davis of England, who didn't even get to tee off on Friday, but came back from two days off to post a 69.
Scotland's Colin Montgomerie climbed up the leaderboard with a 64 - his best effort on US soil - for seven-under 135, where he was joined by American JL Lewis (65).
Tiger Woods, seeking to regain the world number one ranking he surrendered to Vijay Singh last year, was four shots off the pace after a one-under 70 that included double-bogey six at the 18th hole.
That put him in a group of nine players sharing 13th place on five-under 137.