[acidrain]

The bubbles aren't really an indication of anodizing... sometimes they bubble, and sometimes not.
You need agitation...yeah, the air stone is a joke... make a PVC pipe that goes across the bottom of the tank with a small hole drilled at the part locations. Bigger bubbles are better.
As for the parts turning out differently, you might of lost connection. A good way to tell if something is/has gone wrong is to make careful notes. I've anodized hundreds if not thousands of parts, and I always do this. I use a dry erase board with a chart and just fill in the blanks. Basically, make a chart that keeps track of time, tank temperature, amps and volts. If you see the volts suddenly jump, or start out too high, that is an indication of lost connection. The result will be the three parts with good connection will take dye very well, but might have dissolution from over-anodizing.
When sealing, always pull the parts out and immediately dunk in water. Don't let the sealer dry on the parts as you know what happens.
It sounds like you have a good grasp of the process. The only thing I would suggest is to try going with titanium wire, You can make some inside and outside clamps that hold really well for not much more that a couple of runs of disposable aluminum wire. 3' x 1/16in type I, II Ti welding rod is about $3 each. 1/8in is about $3 per foot.