Regarding the problem the OP is having here, if the web along the rod groove is already a minimum acceptable thickness, then deepening the barrel mortise may or may not work well. If you only deepen it at the breech, then you will have a fulcrum/see-saw hump around the entry pipe. Normally, if deepening a barrel mortise, the whole mortise has to be deepened, either all to the same depth, or at least a long wedge has to be removed from the breech to the muzzle, so as to avoid creating a fulcrum. In some situations the forestock may be flexible enough to work with a slight fulcrum, but getting a barrel seated with a fulcrum in there is not easy. Much easier if there is none.
Another question to consider is whether you are working with a slab or with a precarve. If a slab, and if you haven't yet cut the buttstock profile, then you have more wiggle room. You can drop the barrel deeper and then when the barrel is in place, you then draw the buttstock onto the slab in relation to the barrel. (I don't draw in my final "cut here" lines until the barrel and rod hole are both situated.)
If you are working with a precarve, then you don't have (or may not have) a lot of wiggle room. If you drop the barrel deeper at the breech, it will slightly change your drop at the butt and bring the cheek piece up higher. So, before cutting, it might be helpful to draw it all out on a big piece of butcher paper, just to see what the effect would be.
So, in situations where it won't work to deepen the barrel mortise, another option is to plug the hole with a dowel rod, then redrill. Of course, if you put a dowel in there try to match density if you can. If the plug has a different density than the wood of the stock, then you may have trouble getting the drill to go where you want. The drill may try to avoid the dowel, or it may try to follow the dowel, depending on density.
An option I have heard described, but haven't tried myself, is to make a dowel plug with a deep groove cut down one side. When it is all glued in place that groove will serve as a pilot for where you want the second drilling to go. Before gluing the dowel in place, fill the groove with something soft that won't allow glue to run in there--something like a strip of closed cell packing material. That be soft enough to still let the groove serve as a pilot hole, while being dense enough to keep the glue from running into the groove when you glue the whole thing in place. (Cutting a groove in a dowel rod may itself be a bit of a challenge. I can think of several ways to do it, but I think the safest would be with a Dremel tool. Again, I haven't tried this. Just heard about it. So I'm sorry that I'm lacking details. Maybe someone on here has done this and can comment on their experience?)
