But there are three pairings tied for second, suggesting a nerve-jangling final round awaits them in their quest to win the eighth iteration of the Challenge.
Lee and Whittaker added 42pts at Moortown to the 45 yielded by Ganton on day one, four birdies helping them to a 22pt haul on the way out. Whittaker was responsible for 18 of the 20 earned on the back nine.
Hoping to chase them down on Friday, all starting on 83pts, are James Foley and Martin Jackson (Hollywood), Rudding Park's John Macnamara and Richard Pallister, and Aaron Leathley and John Kennedy, of Consett.
Howley Hall's Jamie Poyner and Stephen Bestwick, the first-round pacesetters, are a further three points back having compiled a comparatively meagre 33 at Ganton after leaving Lindrick with 47pts.
Foley and Jackson, after claiming 41pts at Moortown, produced the best performance of the day at Lindrick, going one point better. The former birdied the par-4 second for a net eagle and added a gross birdie at the par-3 third.
Jackson got in on the act with a net birdie at the par-4 fifth, but three one-pointers in the next four holes slowed their momentum, albeit temporarily as they bagged five more birdies on the homeward run.
Macnamara and Palliser tacked on 41pts at Ganton to the 42 produced at Lindrick, Pallister augmenting five birdies with a net eagle at the par-5 ninth.
Leathley and Kennedy mirrored the daily totals of Macnamara and Pallister, seven birdies being accrued on day two including a run of three in four holes from the third at Ganton, where the best score of day two came from Bradford's Craig Smith and Guy Hammond. Their 42pt tally was set up by three birdies in a row from the fourth, Hammond adding a net eagle at the par-5 ninth ahead of four more birdies going down on the card for the back nine.
Harry Kakoullis (Turton) and Kevan Yardley (Horwich) were the top performers on Thursday at Moortown with 44. They had four birdies and each of them contributed a net eagle.
Each duo is competing for daily prizes, series supremacy and the overall title, won last year by Hessle's Rodney Shimwell and Andrew Greetham.
There are three series, each named after the course on which the pairings begin their journey in pursuit of glory in a competition that has become more popular year-by-year since its inception in 2013.
Lindrick head professional John King was one of the men behind the concept, which was born during a marketing committee meeting looking at ways of attracting players to the three Ryder Cup venues with which the area is blessed. His former assistant Luke Allen continues to act as the tournament's administrator following his move to join the Peter Cowen Golf Academy.