I have one of those doweling jigs. They work well for alignment. On the other hand I wouldn't spend the time nor money widening jambs if they will be stained. Pine jambs are too cheap (inexpensive), and hanging a door is too easy, to waste time and money �making do�. And why would you extend the face side in the first place. Wider jambs are available.

I know there are pegs that sit in the door that keeps them in the tracks. Will cutting the doors cause any problems regarding this??

You apparently had bypass doors on the closet. Most bifold doors available at home stores are really cheap and do not have enough wood to allow trimming to fit the 47 opening. Better quality doors cost in the neighborhood of $300+ for a set, but they have wide stiles that will allow trimming. If there are no kids/teenagers, the cheap doors will allow 1/8 removal(usually only 1 1/8 to start) per door section. But they will not take a lot of abuse.