What makes you think you have a headspace problem?
In my experience, Krag barrel index marks usually line-up with the receiver index mark, when putting a loose barrel on a receiver.
(BTW - Early barrels have a 'flat' breech-face and need the rear barrel-thread to be slightly 'beveled', in order to fully seat against the inside flange of later model 1898 & 1899 receivers).
Krag index marks need to line-up for the sight-screw holes & front-sight to be 'plumb'. This is also required in order for the extractor-notch to properly line-up.
Krag headspace is surprisingly tolerant and easily solved by switching to a 'newish' bolt.
Most Krag bolts will not close on a .073 inch thick 'Field Gauge', which is a better standard for Krags than a 'No-Go Gauge).