RFID Code (and setup) works on an UNO but not on the Yun

Question

We're using two RDM6300 RFID readers for this, and the code works when plugged into an UNO, but not when connected to the Yun. We have one of the rfids plugged into the rx pin (0 on the digital side) and the other plugged into pin 2 (same exact way we had it working on the UNO). Anyway, is there something majorly different between working with just sketches on Yun vs UNO? This code doesn't even involve using the Linux side yet as we couldn't get this major part figured out. Any help would be appreciated

#include <SoftwareSerial.h>

    //2nd RFID using SoftwareSerial
    SoftwareSerial RFID(2, 3); // RX and TX


    // define constants for pins
    int UNLOCK = 8;

    // variables to keep state
    int readVal = 0; // individual character read from serial
    unsigned int readData[10]; // data read from serial
    int counter = -1; // counter to keep position in the buffer
    char tagId[11]; // final tag ID converted to a string

    char* authorizedTags[4]; // array to hold the list of authorized tags

    // fills the list of authorzied tags
    void initAuthorizedTags() {
      //tags
      authorizedTags[0] = "02006750B7"; 
      authorizedTags[1] = "02006750B1";
      authorizedTags[2] = "02006750B2";
      authorizedTags[3] = "02006750B3";
      authorizedTags[4] = "02006750B4";
    }

    void setup() {                
      Serial.begin(9600);

      //start serial to RFID reader2
      RFID.begin(9600); 


      pinMode(UNLOCK, OUTPUT);
    //  pinMode(SUCCESS, OUTPUT);
    //  pinMode(ERROR, OUTPUT);
      initAuthorizedTags();
    }

    // check if the tag ID we just read is any of the authorized tags
    int checkTag() {
      int i;

      for (i = 0; i < 4; ++i) {
        if (strcmp(authorizedTags[i], tagId) == 0) {
          return 1;
        }
      }
      return 0;
    }

    // convert the int values read from serial to ASCII chars
    void parseTag() {
      int i;
      for (i = 0; i < 10; ++i) {
        tagId[i] = readData[i];
      }
      tagId[10] = 0;
    }

    // once a whole tag is read, process it
    void processTag() {
      // convert id to a string
      parseTag();

      // print it
      printTag();

      // check if the tag is authorized
      if (checkTag() == 1) {
        tagSuccess(); // unlock solenoid
      } else {
        tagFailed(); 
      }
    }

    void printTag() {
      Serial.print("Tag value: ");
      Serial.println(tagId);
    }

    // perform an action when an authorized tag was read
    void tagSuccess() {
      Serial.println("Tag authorized.");


      //activate solenoid, 
      digitalWrite(8, HIGH);
      delay(3000);
      digitalWrite(8, LOW);
    }

    // inform the user that the tag is not authorized
    void tagFailed() {
      Serial.println("Unauthorized access!");

    }

    // this function clears the rest of data on the serial, to prevent multiple scans
    void clearSerial() {
      while (Serial.read() >= 0) {
        ; // do nothing
      }
    }

    void loop() {


    //RFID 1
      if (Serial.available() > 0) {


        // read the incoming byte:
        readVal = Serial.read();

        // a "2" signals the beginning of a tag
        if (readVal == 2) {
          counter = 0; // start reading
        } 
        // a "3" signals the end of a tag
        else if (readVal == 3) {
          // process the tag we just read
          processTag();

          // clear serial to prevent multiple reads
          clearSerial();

          // reset reading state
          counter = -1;
        }
        // if we are in the middle of reading a tag
        else if (counter >= 0) {
          // save valuee
          readData[counter] = readVal;

          // increment counter
          ++counter;
        } 
      }

    if (RFID.available() > 0) 
    {
        // read the incoming byte:
        readVal = RFID.read();

        // a "2" signals the beginning of a tag
        if (readVal == 2) {
          counter = 0; // start reading
        } 
        // a "3" signals the end of a tag
        else if (readVal == 3) {
          // process the tag we just read
          processTag();

          // clear serial to prevent multiple reads
          clearSerial();

          // reset reading state
          counter = -1;
        }
        // if we are in the middle of reading a tag
        else if (counter >= 0) {
          // save valuee
          readData[counter] = readVal;

          // increment counter
          ++counter;
        } 
    }


    }