IrishGirl, I don't know anything about PKD that I have not learned on this site, so I will leave that for the more informed among us.
I do know a bit about transplants from living donors, though (I've had two), and can share about that. If there is ANY reason to eliminate someone as a living donor, it is the transplant team's job to find it. High blood pressure, which can either lead to or be an indication of kidney disease, depending on who you talk to, is usually the first thing that will disqualify someone as a donor. Diabetes or a strong family history of diabetes is another. Unfortunately, a family history of PKD (especially a strong one like your's), even if the individual does not have it, will also eliminate someone as a donor. The process of testing potential donors is to screen for potential problems in the donor which could cause problems if the donor was to end up with kidney problems later.
Even if you were unable to donate to your son (IF he ever needs it, praying for the opposite!), what about his father or an aunt or uncle from his father's side? Also, more and more non-related living donor transplants are being done - teachers, coaches, ministers, friends and spouses are just a few of those who donate. So don't give up, ok?