Striker Waghorn and defender Kiernan were ineligible to feature in the FA Cup semi-final against Arsenal at Wembley last Saturday having featured for other teams earlier in the competition.
The two have been among Latics' more impressive performers in recent weeks and could both slot straight into the starting line-up along with goalkeeper Ali Al Habsi, who is expected to dislodge Scott Carson between the sticks.
Midfielder Roger Espinoza (hernia) is training again but winger Callum McManaman, who won a penalty against the Gunners, may revert back to the bench after being withdrawn at Wembley because of cramp. Ben Watson (broken leg) and Chris McCann (knee) remain long-term absentees.
Reading head to Wigan with a mounting injury list to contend with.
Hope Akpan (ankle), Danny Guthrie (calf) and Jem Karacan (knee) missed Monday night's 1-1 draw against Leicester while fellow midfielders Danny Williams (knee) and Garath McCleary (back) were patched up to play, only to suffer recurrences of their injuries.
Winger Jordan Obita also had to go off with a calf problem so boss Nigel Adkins admits he will have to hold a roll call ahead of the trip.
To make matters worse midfielder Mikele Leigertwood, thrown into action as a sub on Monday after a year out with an ankle injury, got himself sent off and serves a one-match ban.