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From the doctor's line "not nearer to the machine's location", one might think that he thinks the purpose of the simulations is to find the machine; however, it is unclear just how much the doctor himself knows, e.g., about what Shaw can know. Greer and Samaritan (GaS), on the other hand, definitely know and can infer a few things: Throughout season 4, Team ...


Finch never referred to the Machine as a "she" until after Root did it; it appears to be something he has picked up from her. Before Root effectively assigned a gender to the Machine, Finch and Reese always simply used "it" or "the Machine" with no sense of any familiarity. Now that it seems likely that the use of "she" will stick.


He had visited the cafe as Harold Finch previously and made the same order with Grace. He then repeated the visit in his Professor Whistler identity and was recognised by the waitress. Samaritan could hear what the waitress said to him as well. Enough was the same for Samaritan to draw a line between the two identities. Bear in mind, in an early episode ...


The mysterious criminal mastermind known as The Voice has returned in the fifth season, in the Sotto Voce episode (S05E09). A bit more detailed answer with spoilers:

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