An oval bore ? I never heard of such a thing or how it would happen short of running it over with a tank . Type 38 rifles all have an oversized chamber , made worse by shooting undersized Norma ammo . The case comes out looking oval . That is not a headspace problem . I think you might need a new gunsmith ?
The quality control late in the war was almost non-existent. If it would chamber and fire a round, it passed muster at that time and place.
I had an Arisaka that was rebarreled for 7x57. It was quite accurate but had feeding issues and looked pretty ugly. A girlfriend ran off with it, and I philosophically decided to consider it a favor on her part.
Since Type -38 6.5 mm rifle production quit near the start of the war , what you said does not apply in this case .