The veteran midfielder missed United's Champions League draw against Real Madrid at the Bernabeu on Wednesday because he is carrying a knee injury and he will miss the cup tie with the Royals as he faces two more weeks on the sidelines.
However, with a full weekend to prepare his side for the game against their Premier League opponents, Ferguson revealed at his Friday morning press conference that everyone involved in midweek has returned with no injury problems.
But with the Red Devils fighting for honours on three fronts, he is set to utilise his squad to the full against Brian McDermott's Royals.
Ferguson said: "We've come through Wednesday night's game with any injuries. That's the best thing, apart from the result of course.
"Of course, I'll make some changes for Monday night, even though it's an incentive to get to the quarter-final. I don't think that's lost on any of the players.
"I think there's a good spirit in place and they're all contributing. Whatever side I pick we're expected to qualify. That's what happens at United. Whatever team you play you're always expected to win.
"I went to see Reading last week and they're a team who are showing plenty of fighting qualities at the moment, as you'd expect given they're down the bottom of the league.
"We'll take nothing for granted. In the FA Cup you always expect the unexpected. It happens so many times. You just hope you're not a casualty or a shock. We've had a few over the years.
"But I can't be more pleased than I am at the moment with the form and spirit in the place. It's good."