That left the youngster from Northern Ireland nine shots behind compatriot Clarke, who was one under for his round and five under overall with four holes remaining.
Clarke made a flying start with a birdie at the first from 15 feet, but missed from less than half the distance for another on the next and even shorter on the fourth.
Three putts on the fifth cost Clarke a bogey, but he bounced back with a birdie on the downwind seventh before dropping another shot on the eighth.
The 42 year old had shrugged off the forecast bad weather as "just another Portrush" day, but in truth the conditions had eased considerably for the later starters.
Clarke took advantage with a birdie on the 12th and at five under par was one clear of American Dustin Johnson, with first-round joint leader Thomas Björn a shot further back.
Earlier in the day, 61 year old Tom Watson used all his experience to defy the conditions and card a brilliant 72.
Watson, who carded the 15th hole-in-one of his career in the second round, opened with six straight pars before taking advantage of the downwind par five seventh, finding the green in two and two-putting for birdie.
Fellow American Gary Woodland had been the only other player to break par on the front nine at that point, the 27 year old out in a remarkable 33 after birdies at the fifth and seventh before coming home in 41.
Three bogeys in five holes on the back nine halted Watson's progress, but the five-time Open Champion holed from 20 feet for birdie on the 16th before three-putting for bogey on the 18th from just short of the green.
It took almost two hours before his four over par total was beaten by France's Raphaël Jacquelin, but with the weather easing, a repeat of 2009 - when Watson had a putt to win on the 72nd hole before losing in a play-off - was unlikely.