The protocol for Krag sporters since the beginning of time was to put a barrel band on to anchor a screw into up through the fore arm. Some crafty guys even d/t'ed a screw hole under the receiver ring (but that's darned difficult as the steel is harder than woodpecker lips). Sometimes you'll see them with a shallow dovetail cut in the bottom of the barrel into which a block of steel is fitted to accept a screw. Any way you do it, the front end of the gun must be anchored. The two trigger guard screws aren't enough - the barreled action will try lever itself up and back out of the wood with each shot with it merely anchored in the back end.
You say the gun is shooting low. Dumb question, but did you raise the rear sight staff to compensate before filing on the front sight? I've owned a pile of Krag Sporters in my life, including a couple right now, and they all had receiver sights on them - and I never ever had to mess with front sights, even issue front sights. If the answer is "yes, I have tried raising the rear sight slide", then I would throw a straight edge on the barrel or something, to make sure the barrel isn't bent down slightly.