The copper and CLR question is very convoluted. On the one hand, you have the directions on the bottle itself that say do not use on copper.
On the other hand, I soaked a penny overnight in the stuff and it didn't do a thing (that I could tell) to the penny. Nothing. :shrug:
So my suspicion is along the lines of the "tarnish" factor that was brought up earlier in this thread. I'm guessing those instructions on the bottle are aimed at people with those pretty copper pots and pans that they like to have shiny looking to hang on their too cool display rack hanging in their kitchen. I don't particularly care if my wb is a shade darker than it was before CLR.
My wb had become really pretty gunked up looking (once I got it clean, I realized how bad it had become). I too tried vinegar which seemed to get about 2 percent of the gunk off. Not enough. Since I have anodized aluminum in my setup, I disconnected just the portion of my circuit containing the wb and fed it some clr and let it soak for about 10 minutes then drained and ran a bunch of water (first a ton of tap then some distilled to flush the tap) and cried with joy at how purdy my wb was looking after that.
Also, I too got bitten by the water wetter residue from hell and nothing seemed to strip that stuff off but CLR. At the time, my entire setup was all copper and I simply added about a capfull or so to my water mix and ran like that for about an hour. It worked like magic on the WW residue. I have no information about CLR's efficacy on biological problems, certainly airspirits witches brew does a smash up job on that type of problem. (my personal variation is more of a 50/50 mix of pine-sol and lysol as opposed to his 90/10). Works great for me.
From my personal experience and what I've gleaned from this and other forums, I conclude that if your setup is all copper or copper and brass, you can run CLR in your mix as a general clean out for things non biological. If aluminum is in the mix, you either have to do an isolated clean or post back to this forum asking for a CLR alternative.