The first thing to take into consideration is the frame ramp is cut for the 45 and not the 40, this can cause feed issues if you are wanting to use a standard barrel.
To solve this problem the frame can be milled for a ramped barrel. I highly recommend barrels with the Para style ramp, because of the radius design.
If you want the most reliable gun it would be best to build a complete 40 topend, slide, barrel, firing pin, recoil system, and extractor.
Also it will be best to change out the 45 ejector in the frame for an extended one designed to work with the 40.
I will say once you start adding up the cost of doing the above you will most likely be able to buy a gun that's already the caliber you want.
I'll second Hunter. It would be an interesting project, but after replacing the slide 'n barrel assembly and ejector, you're into it for darn near the price of another pistol. That's without considering any frame ramp issues (tho back in the day we were able to switch to 9x19mm without changing the frame).
I'd rather just have the second pistol , but hey, that's me.
I don't know of a major manufacture offering a true Commander size gun in 40cal at this time.
That being said I plan on bringing out a new line of custom built single stack guns, in that line will be true Commander size guns.
Building one in 40 cal would not be a problem.
Regards
Bob Hunter www.huntercustoms.com