Code:

paste file1 file2 | awk -F '\t' '
{
  fnum1 = split($1,a,",")
  fnum2 = split($2,b,",")

  linediff=0
  f=0
  while ( ++f <= fnum1 ) {
    if ( a[f] != b[f] ) { ++diff[f]; ++linediff }
  }
}
END {
  while ( ++n <= fnum1 ) {
    print n,diff[n]+0
  }
}
'