Hi Wesg,
It's usually best to square things to the surface that's hardest to change. In a bolt action, it's always the bolt raceway, and in the Ruger with its 90-degree vertical block mortise, it's sometimes the mortise itself. If the barrel is pointing upward, it's easier to use the threads as a reference and change the receiver face and breech face to match, but if the barrel is pointing downwards you need to change the threads. A diagram will help here for clearer understanding.

What's important is that the breechface ends up perpendicular to the bore line (for square case heads) and that the barrel seats squarely against the front of the receiver (even pressure all around the shoulder for even bbl whip). It's not necessary for the breechface to match the mortise or front of the receiver ring, but it IS necessary for it to match the bore line.

If you have to change the threads then you have my deepest sympathy, it's not a job I would tackle lightly. It ain't that hard in a bolt action where the bolt raceway is easy to index from, but a single shot is another story.
Good luck, Joe

This is the last I'll bore ya'll with the details of this.

I trued one face of the receiver to the mandrel. It took less than a dozen strokes on some 400 wet/dry to get it straight. I clamped that face to an angle plate to check the rest. The breech block mortise has a 3° draft, so I indicated that in with a 3° angle block. I put the breech block in far enough that it was supported, and I could still indicate the face of it. It was within .0005 at any point. Just for fun I ran the indicator on the receiver face. I was surprised it was also within .0005.

I checked the thread, crudely, by standing a square next to it and eyeballing the gap top and bottom with a pair of calipers. It calculated out to about 3/4°, pointing down.

So, with the rest of it checking out so close to perfect, it's pretty obvious I have to recut the thread to make it right. I'm guessing I'll have to go at least .030 oversize to clean it up. That's not too bad. I had to take .045 out of my M-70 to get it straight.