1) usually what I do is get a 5g bucket and fill it up 1/2 to 3/4 full of sand and then keep a hose in it until the other 1/2 or 1/4 of the bucket is clear with no excess particles. Repeat this process until you have enough sand for your tank.
2) No your polys won't be harmed. They might be a little stressed out, but after a couple days they won't remember a thing.
3) The sand (unless you are getting it already wetted down and used) most likely will not have parasites, and even if it does they will most likely not be anything that can translate to your bichirs. One thing I would watch for is the kind of sand you use and if it has any harmful chemicals/ingredients.
4) Almost all polys get darker when on black sand. Upper jaws tend to get dark and exhibit green pigments. The amount of green pigmentation varies from polys to poly. On Lower jaws they usually get really dark and faded. There are some laps that excel on black sand, but most times all lower jaws look faded and leave more to be desired on black.