Kishi showed his RIGHT EYE when he put Bee in a genjutsu, then the illusion was all black, just like Itachi's tsukyomi. What more proof do you need. He doesn't yell amaterasu when he performs it everytime.
I personally think that blaze release is an advanced amaterasu. It is the technique he realized he could control. I'm sure Itachi had a similar realization with tsukyomi.
As for Shisui, who the hell knows, all we know about him is the fact that he had KA. He most likely only had MS for a short period of time before his death, since him and Itachi were close in age.
There is more to Tsukuyomi, then the inverted colors to. When Tsukuyomi is used the recipient's validity of time is changed, and more.