Clean Sediment & Minerals from Water Lines?

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Nova Scotia
While we were installing our water softener and cutting open the lines, we noticed that inside the lines it was black/brown/reddish and slimy and there was a build-up of sediment.

We are on well water. We have a Big Blue sediment filter. We installed the softener, not just to get rid of hard water, but to remove manganese (around 1.5 ppm and iron 0.5 ppm; this was what it was AFTER the sediment filter).

How would we go about flushing the lines clean? Pouring vinegar down the well? CLR? I know bleach will kill any manganese/iron bacteria (though I don't know why we would have bacteria when we had and still have a UV light), but I want to remove the sediment in there.
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