Check the torque of the crank to the chainrings and also the pedals to cranks. If those check out then move to seatpost and stem/headset as you weightshift might be causing the issue per pedal revolution.

Also, since the bike has been ridden some, I'd go ahead and retorque all the suspension pivots in the back end. I've found this really brings back that sharp taut ride to a full suspension bike.