[XSleeper]

You say it's "rubbing" but that doesn't tell us a lot. Is the gap on one side larger, and it's rubbing on just one side? Or is it rubbing on both sides? If its rubbing on both sides, the doors are thicker. Such as 1 3/4 instead of 1 3/8. But if it's only rubbing on one side, that is due to where you mounted the rollers. And is it rubbing only in one spot, or is it tight all along the side of the door?

Sounds to me like you have installed the rollers in the wrong spot, which moves the doors more to one side than the other.

You said the doors are exactly the same size, then on another line you ask if they could be thicker than the old ones... so which is it? As 1865wingate said, you can put a straightedge like a 2 ft level on the raised panels and see if they stick out farther than the door edges. Only you can answer that.

If its only rubbing a little bit you can remove the 2 stops that the door passes between and rip them down on a table saw so that the door doesn't rub on them. That means taking off the casing and the stops.

 

[XSleeper]

On older pocket doors you sometimes don't get the rollers to hang in the track right, and they ride on the lip of the track rather than in the bottom of the track where they are supposed to be seated.

That would also throw the door off to one side. And it might eventually fall down into the track where it's supposed to be, as you use it a few times.

 

[XSleeper]

Yes, 1 3/8" is the thinnest door that is commonly sold. The other common size is 1 3/4". I don't think you would want to hang a 3/4" panel there since they tend to warp. That would be cut from a 4x8x3/4" sheet. Plywood tends to warp, but fiber core (MDF core) lays flatter. It's not the best material to hold a screw either, you definitely need to predrill it.

 

[XSleeper]

If its only rubbing a little bit you can remove the 2 stops that the door passes between and rip them down on a table saw so that the door doesn't rub on them. That means taking off the casing and the stops.

 

[XSleeper]

Well they are 1x2 or 1x4 not 2x4, and you aren't going to stick your arm in there and do much of anything. If you need to repair the pocket door framing, you'd have to remove the drywall on one side to do it.