Chelsea host Wolverhampton Wanderers on Saturday and will expect to chalk up their fifth successive home league win, which would put them eight points ahead of United.
It emerged this week that the manager had known as early as August about Rooney's intention to leave and that distraction, combined with the poor form of the England striker - who is out this week with an ankle injury - can hardly have helped his team-building plans.
Ferguson was meeting chief executive David Gill later on Thursday in an attempt to find a way of drawing a line under the Rooney issue.
"We don't want this to carry on. We don't want it to become a saga," Ferguson said. "We've got the team to consider and an important game on Sunday.
"If we carry on talking about one individual, dominating all of the headlines and all of our thoughts, then we're not doing our job."
Ferguson rested Dimitar Berbatov and brought Javier Hernandez off the bench for the last 12 minutes of Wednesday's 1-0 Champions League win over Bursaspor but Federico Macheda did not exactly grasp his opportunity as he failed to spark in a lone striker's role.
With Ryan Giggs joining Rooney in the treatment room Ferguson has some juggling to do for what will be a real test of his side's mettle.
Since Stoke returned to the Premier League in 2008 United have won all four games against them but Stoke have started well this year and are ninth in the standings.
United, after drawing at Fulham, Everton, Bolton Wanderers and Sunderland this season, as well as being held at home by West Bromwich Albion last week, will travel nervously while combative Stoke will relish a chance to add to Ferguson's woes.
Chelsea were short of players and short of inspiration in their goalless draw at Aston Villa last week and they will hope that Didier Drogba, at least, is fit to return against Wolves.
Hard on Chelsea's heels are Manchester City, who play third-placed Arsenal in an intriguing clash at Eastlands on Sunday.
City, with Carlos Tevez in great touch, are gradually settling into a recognisable team and though they often seem to make hard work of dismissing lesser opponents, in contrast to many occasions last season, they are finding a way to do so.
By the time Liverpool host Blackburn Rovers on Sunday they could well be bottom of the league. They are above West Ham United only on goal difference and the Londoners can add to their six-point tally at home to Newcastle United on Saturday.
Liverpool failed miserably to rise to the occasion of last weekend's Merseyside derby and were well beaten 2-0 by Everton.
They have won only one game all season, key striker Fernando Torres still looks hopelessly off the pace and new signing Joe Cole has been anonymous as he struggles with what he describes as the worst run of form of his career.
Liverpool will have limited rest having travelled back from playing Napoli in the E
