I can help with some, but not all of your questions.
1. For the nice, deep reds that I achieve, I will dip my parts in the red dye for 3-5 minutes, then rinse in cold water. I've noticed that red alone is not deep enough for my tastes. I then dip the part in HBL black for a few seconds, usually 5-30, then rinse again. This will take the part to a much darker color, somewhat of a burgundy. I then dunk in the red dye for another 10-15 minutes to allow the part to soak up as much red as possible. What I end up with is a very nice red that suits my taste. There's some pics floating around in a thread somewhere if you'd like to see.
Another option: mix some black dye in with the red. This might help you, but I would recommend doing this in small steps.
2. I've never used Caswell's Desmut, but I believe it would be best to have the parts as clean as possible before desmutting. Possibly a good hot water/soap wash before desmutting would not be overkill.
3. Different aluminum alloys may cause this. Also, you may just have some dye left on the surface after sealing. What was the surface finish on the chalky parts before anodizing? Gloss, satin, or matte?
4. I've never tried anodizing different series of aluminum in the same batch, so I won't comment on this. It would only be a hunch.
5. The black residue on the parts should easily clean off under running water with a cloth or toothbrush immediately after stripping. Less time in the stripper will help minimize this.
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