Try just closing a bare bolt (striker/extractor mechanism removed) in the action.

This will tell, if it is a bolt fit problem. (Very unlikely)

If the bare bolt closes. Try closing the bare bolt on a cartridge. This will check chamber dimension and minimum head-space. (Usually checked by barrel installer with a 'Go Gauge').

If the bare bolt closes on a cartridge, then the problem is likely with the extractor or 'extractor cut'. (Something interfering with the extractor being free to rise and snap over the cartridge rim).

Do your cartridge cases have a bevel on the rim?

(IIRC - Someone recently had a problem with Hornady .30-40 Brass, which was lacking the traditional bevel. The case bevel assists in the extractor 'claw' moving upward).

BTW - There is a slight inclined edge or shelf on the left interior of the Krag action.
The left edge of the extractor-spring rides under this surface to assist keeping downward tension on the extractor 'claw'. Check these surfaces for burrs or debris.

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