Your chameleon is shedding it's skin. This happens to reptiles when they outgrow their skin and will happen throughout their lives. It's nothing to worry about just means he is growing. They shed more often when they are younger.
if its not red, and its not dried poop, then its probably a sperm plug, so no worries on that.
Next, yes I would block their views from each other.
Chams should not see other chams unless they are going to be bred.
Are you going to breed him?
Yes thats a sperm plug... And if he can see your female its not a huge deal if you don't notice behavioral changes such as him in mating colors going bonkers in his cage... You should be able to tell stress or whether or not he can see a female...