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the higher the PT Score the better; i had picked up a couple of random Gold mares and got some Intact colts from the booststrap pairings ; they PT Scored higher than the father did so i replaced him with them

Just remember that PT score is related to performance and is not necessarily and indication of breeding ability. They are slightly correlated - Star-papered stallions tend to have higher PT scores than yellow papered - but between two Star-papered stallions, the higher PT score is not necessarily going to produce the best offspring.

There is a very big difference between the best stars and the worst stars. You'll probably need a couple generations before you are able to put bootstrapped foals through Breeding Advice.

What I did was I didn't do breeding advice on the fillies - just sorted them by paper and genetics, but did run BA on the colts. Once a good chunk of my colts were passing BA, I started running BA on the ladies. That way, you can keep progressing your mare quality (and thus foal quality) and get higher gold mares to breed with your star stallions. Once the colts start passing BA, then can start being compared to sire to see if they can replace him as herd sire.