aqua mira worked great for me on the pct in 2004. make sure to carry at least two mixing caps with you (just put one on each of the bottles) so you can make more water at the same time.
i had very few issues with floaties and funk in the water. if i ever did, i'd strain it through a bandana and no worries. once we had to get super-funky water from a water cache at hat creek rim for someone who ran out. it was last year's water cache water, and full of serious gunk. we strained it through a bandana, pumped it through someone's water filter, and then aqua mira'd it.
i also had basically no problems with getting water anywhere with just the usual aqua fina 1L bottles and a 2 or 3L platypus. i didn't see any need for aluminum tubes, straws, or anything else.
i worried about water before my hike started, but you quickly get very adept at dealing with it all - camping at water or cooking dinner when it's around (if if it's 2 pm), camel-ing up when it's available, and carrying just what you need to get to the next reliable one.
have a great time!