Fogarty and Wighton had struck up a positive partnership in the halves over the past 18 months before Stuart shook things up in August by handing Matt Frawley the No. 6 jersey.
Wighton, who will leave Canberra for South Sydney next year, has had to make do at centre - where he last played regularly for Canberra in 2014 - taking over the position from the dropped Jarrod Croker.
While Stuart has pointed out Wighton has represented NSW and Australia in the role, the late shift is perplexing given the Raiders have spent the past five years picking him in the halves.
Frawley and Fogarty have started just three games as the club's halves pairing this season, with their sole win coming at home against struggling Canterbury.
But Fogarty was confident they were finding a good chemistry ahead of Sunday's elimination final away to Newcastle, underlining that they had matched it with Brisbane and Cronulla until late dismissals turned those games against them.
"The last two weeks we've been in the game right until the end and we've had guys go off," Fogarty told AAP.
"He (Stuart) didn't ask us about it. He's the coach, he makes all the decisions and he said: 'This is what the team is and this is what I think the best is for us going forward'.
"It sucks, because all us boys love playing with (centre) Jarrod Croker and we want him to be in our team.
"At the end of the day the coach is the coach and we have to support his decision, be professional and get on with it."
Depleted by an arm injury to Josh Papalli and suspensions to Corey Horsburgh and Sebastian Kris, the Raiders face an uphill battle to defeat Newcastle.
The Knights have hit a hot streak and will be seeking a 10th straight win when the Raiders, who they have defeated twice in the regular season, roll into town.
Fogarty has admired Newcastle's late-season surge from afar and said they could punish any side who wasn't on their game.
"They can attack from tryline to tryline," Fogarty said. "Dominic Young, Kalyn Ponga and Greg Marzhew - they're a real threat.
"Adam Elliott has really added to them in the middle. Since he's come back they've been a different team.
"It's a big challenge going up there this weekend to a hostile environment."
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