Two-grouping is, from my experiences, usually always caused by an uneven stress at some point between the barreled action and the stock. Rugers are a little more difficult to "tune up" than most others, due to the angled front bedding screw and a usually ratty trigger pull. One thing you want to make certain of is that the recoil lug has clearance on both sides as well as the front surface and the bottom. The only place you want full contact with the stock is on the back side of the recoil lug. If your gun has a screw in front of the trigger guard, make certain it is not overly tight, as this can tend to warp the action to a slight degree, and cause inaccuracy also. I also solid- bed about 2" of the barrel in front of the recoil lug, and free-float it the rest of the way, giving ample clearance between the barrel and stock in the free-float area. Bedding the action at the same time as the barrel is probably the best way to go, but as stated before, go slowly, and think about the consequeces of your actions and use a little common sense. You should be able to handle this just fine.
The method I have described is how I've done Rugers over the years, and is only my way of doing it. Accuracy was improved on most that I've bedded this way, but there are those out there that will just not shoot for whatever reason, and are good trading stock only. Good luck, and keep plugging along............