Thanks for the reply.  That was about the point I was at when I posted, but I kept hitting various special case situations that broke the algorithm. Here's what I ended up with. It seems to be consistent.

Each input array has a matching 'chosen' array that keeps track of which elements have been used already.
Then a single loop checks for '2s' first.
Then the double loop checks the remaining elements for '1s'.


int[] a1;//input 1
int[] a2;//input 2
int[] a3;//output
int[] a4;//set to 0 when a2 used
int[] a5;//set to 0 when a1 used
int len; //length of arrays;
int range;//max value for creating random arrays

void setup() {
  len = 5;
  range = 7;
  a1 = new int[len];
  a2 = new int[len];
  a3 = new int[len];
  a4 = new int[len];
  a5 = new int[len];
 
  for (int i=0;i<len;i++) {
    a1[i] = rand(range);
    a2[i] = rand(range);
    a3[i] = 0;
    a4[i] = 1;
    a5[i] = 1;
  }
 
  for(int i=0;i<len;i++){
    if(a1[i]==a2[i]){
      a3[i] = 2;
      a4[i] = 0;
      a5[i] = 0;
    }
  }
 
  for (int i=0;i<len;i++) {
    for (int j=0;j<len;j++) {
      if((a4[j]==1) && (a5[i]==1) && (a1[i]==a2[j])) {
          a3[i] = 1;
          a4[j] = 0;
          a5[i] = 0;
          break;
      }
    }
  }
  for (int i=0;i<len;i++) {
    println(a1[i] +"  "+a2[i]+"  "+a3[i]+"  "+a5[i]+"  "+a4[i]);
  }
  noLoop();
}


int rand(int mx){
  return int(random(mx));
}