There is a little more information needed before anybody should answer on a touchy subject such as this. Has a competent gunsmith looked the gun over for you? Cracked lugs may be rare, but possible. Have you shot any commercial rounds through it already? Some reloading manuals do not suggest going below the starting powder charge as it can lead to other issues.
My Krag was also "sporterized" by shortening the original stock and having a 23-1/2" barrel before I obtained it. I would like to know its history, but will never know. After my Krag was checked out I used the loading tables and stuck with IMR4350 and Hornady 180gr RN interlock. Will you be using your Krag for hunting? I'd like to harvest a deer with mine, it would make a good brush gun.