In "If-Then-Else" when Root gets the instructions, he says "who's she talking to?" so he definitely doesn't know the Machine communicates with Root through an earpiece.

I don't think the cyclist was a Samaritan operative - she was off the grid in that park until someone with a phone hanging on a belt clip happened to have a camera facing her.

Since so much has already been discussed, I'll make one minor point - Shaw was working at Bergdorf Goodman, not a "mall." Root sneaks her out an entrance on 58th Street to the waiting motorcycle.
Earlier in the episode she tells Fusco she works for Estee Lauder, and a previous episode suggested she worked at…