Hi,

1- I remember that once I had to hack a few lines in the assoc.cpp file of PLINK, so I had a look in the code (Plink::correlation2SNP() funtions, called from Plink::calcLDStatistics()) and found the following lines to keep only founders in the analysis:

// Iterate over every individual but only consider founders
  ...   {
  // Allow for 1 or both SNPs to be non-autosomal
  for (int i=0; i < n; i++) {
    Individual * person = sample[i];
    // Only consider founders
    if ( ! person->founder ) continue;

-> yes, I suppose that parental and maternal informations really matter !

2- on the contrary i suppose you do not have to care about the pheotype column in the LD analysis, just put zero for every sample. The --no-pheno option is needed only if you skip the column.