It's perfectly legal to change calibers on an NFA weapons. There's no permanent alteration of the registered part, which, in this case, is the receiver, so there's no technicality you can get in trouble for. If you really, really want to make sure, all you have to do is notify the BATFE in writing that your weapon is multi-caliber. If you want to do that, include calibers it will be used to fire, as well as barrel lengths it will have. But it's really unnecessary, because, like I said, as long as there's no permanent change to the receiver, there's no infringement of the law. If you do decide to notify the BATFE, include your name, the weapon's identification information (SN).

I don't know how effective a short-barreled 5.56mm rifle will be. Correct me if I'm wrong, but as a high-velocity round, a fired 5.56mm bullet achieves most of its energy through velocity, caused by a long barrel? Heck, you might even get some powder going off outside of the barrel if you go short enough.