What I'm going to say will be obvious to the veterans, but just to be sure:
Unfortunately, at times people have neglected to say "your original case", as opposed to your spare. If the oddity is in the block this won't matter, but unless you're sure use the actual parts you will assemble, and make a written record of what you found, what parts were used (I use brand, part number, and a picture), what you did, and how it came out. This pair (block and case) are now "mated"; expect to do it over when you take either one out of service.
In addition to the dial indicator reading, I look for any signs of an irregular casting. Since castings vary somewhat due to production changes, core shift, and individual mold pours, an empty, clean block should be examined carefully for casting accuracy before spending any money. Irregularly cast blocks are more likely to lack concentricity between the cast surface and a machined surface or hole, where the opening is not centered in the boss, the wall is thicker on one side by more than 1∕64”, &c. These tell-tale holes include tappet bores, head bolts, distributor opening, pushrod reliefs, main bearing cap bolts, and oil pan bolts in the block’s pan rails.

The dowels are very useful, but in my experience count on spending time finding the best position - they can be "clocked" with a big screwdriver (even when in place, you may need an assistant for each dowel) to both change the amount of eccentricity (away from the correct location) and the direction of movement.

Don't wait for something to fail. If the visual aren't perfect, or there has been symptoms, fix it while it's still cheap to do so.