That's just the way the cactus are, it's the sign of a healthy cactus. Too much sun and it starts to turn yellow. The blueish tint is very prevalent on peruvianus. It's best to grow them under some sort of partial shading, to maintain the beautiful color. I doubt it indicates alkaloid content, if anything it probably means less than a dried out, yellowed cactus.
The black dots are the result of the plant adjusting to different lighting conditions, transplanting stress maybe. They should scab over in a few days. They'll be fine.
If you're having trouble seperating roots systems, use a hose nozzle and lightly spray the dirt away. Gently seperate them as you do this, it's nice if you have someone helping you.
Wait a week or two after putting it in a new pot of soil before watering it, this gives any root damage you may have caused a chance to heal without growing bacteria/mold, and the roots will go deeper into the soil in search of water.
Personally, Highonlife, I think you should maintain a healthy, happy plant with good vibes for a while before you decide to stress it.
What can anyone tell me about maximizing alkaloid content? I know drying is quite effective, but is that the result of a stressed plant producing more? Or is it simply a chemical conversion that takes place as cactus material dries out? Like, if you let a whole cutting dry out on it's own, vs cutting up a fresh chunk and letting that dry out, how would the results compare?
Also, i've heard of people injecting with dopamine...what can anyone tell me about that?