The only problem I see is with the torch spines growing into the san pedro column, them I would separate if you can. The black spots are bruises as youve said and I dont think you have anything to worry about. Other members will give their advice. They look pretty healthy to me.
Christine

I don't get it. What is the point of grafting a Trichocereus peruvianus onto a Trichocereus pachanoi? Both grow well on their own roots. I am very curious about that.
If this was my plant I would ungraft the scion and root it to get rid of the problem with the spines.

to be honest i dont know why it was grafted, i bought it that way off a seller on ebay. Could I clip the spines, or is ungrafting the only way? I'm only hesitant because I have never cut a cactus, and feel a scared of hurting/killing it