Changing Connecting Rod Bolts.

So the engine you just bought, you pulled apart? It already had .040" over pistons in it?

What do the cylinder walls look like as far as wear and crosshatch?

If as mentioned above, you are just doing a basic rering and the bearings look good, for a daily driver with no intentions of beating it to death I would just run the rods and bolts as is.
However, if you intend to beat on it you might think about new bolts and resizing the old rods or new rods.