how can you index a 9 speed 11-46 tooth cassette if the gears arent equally apart
It sounds like you're talking about the tooth difference, and not the horizontal spacing between cogs.  Most cassettes are &quot;uneven&quot; in this sense.  It does not affect indexed shifting, so long as the derailer can accommodate the max number of links difference and can &quot;reach&quot; as high as the largest cog.