Not a big deal to run run .040 under. Done it before, would do it again.
To me it's no different than running spacers to run a smaller journal crank in a big bore, like a 340 crank in a 360 block.
Make sure your oiling system is up to the task. Drill extra holes in the filter plate is one spot that is very simple.
If you engine makes peak at 6400, don't put a 6500 chip in an MSD unit. They are known to start dropping cylinders a few hundred RPM before the actual rating. Put a 6800 or 6900 chip in the box to get clean ignition signals to 6400, plus a little extra in case you run through the lights at higher than peak rpm.