Cartridge cutoff not working could allow shells to be 'coming up/feeding' before extraction, causing who knows what shell interference when using the lever. Numrich gun parts have a lot of parts.

Is your 99 a tang-mounted safety or is the safety near the lever/trigger?

If chamber is too large it may allow fired brass to expand too much, making action stiff. Steel casing expand differently.

Comparing extraction issues from firing rounds to unfired rounds cycled through isn't a precise comparison. You have to fire both. Did you?