I need help keeping my loop running.

  if (talking == 0 &&  startattempt < 100){
    pinMode(outputpin, OUTPUT); // initialize the digital pin 1 as an output to control communication intialization:
    digitalWrite(outputpin, HIGH);
    delay(300);

Why is setting pin mode conditional? It should always be set, exactly once.

What is the purpose of the delay? Do you like sitting around doing nothing?

The code still runs the loop over and over but, it ignores my "if" statements in the "setup" area of the code.

No, it doesn't. Inside the if statement, you have a while(Serial.available() > 0) statement. Think about whether there is any serial data received yet. You appear to want to wait for a response, but you don't have anything that makes setup() wait for data.

  if (talking == 0 &&  startattempt < 100){

Can they really be anything other than 0? Is this statement accomplishing anything?

      }
    }
      }
    }
  }
}

Nice job of indenting...