Has the engine been rebuilt before? I'm under the impression that it was not, as you started by replacing the bearings with standard size. With a scotch-brite pad, you shouldn't be able to remove any substantial material from the steel crank journal. There should be NO reason to go to a .040 over/undersize.
If your crankshaft is still standard size- putting in an .040 over/under bearing will make physical contact between the rod and crank journals- guaranteeing a burned bearing all over again. Please install your standard bearing again but this time with a piece of "plasti-gauge" and make sure there is only a few thousandths of a gap. That would be best way to ensure you have the right fit.
Dont go with "close". Go with what you know. go with hard numbers.
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