Dh tested negative to 89 mutations prior to conception. After conception we found out that the baby still had a 1/500 chance of having cf. We put that bit of info in the back of our minds and carried on with the pregnancy and didn't worry. After the baby's birth when I felt up for it at 8 wks I took him in for a sweat & genetic sequencing (1000+ mutations). He was totally healthy. The sweat test came back negative within a week or two. The genetic test found a second mutation...other htan the one he inherited from me. It was a shocker for all of us, even the members of this site were taken aback. He is currently assymptomatic but we treat him agressively to prevent any lung damage. We're definitely glad we know.
My guess that there is a large part of the population that carries one of teh 1500 known mutations. I believe the est. of 1 in 23 caucasions is a best guess.
If I had it all to do again (ie were in your shoes) I would do the same thing...test for the 95% (89-97) of the mutations in my spouse and then if negative continue with a pregnancy. At birth (this is the part I would do differently) I would have an Ambry test ready to send off with cord blood for full genetic sequencing.
The reason I wouldn't test for all 1500 mutations right away is because many create an atypical type of cf and although I take this very seriously it is not personally a reason I wouldn't want to bring a first child into the world.
Now that I know our genetic situation things are different because I am at odds with wanting another child (largely so that my son will have a sibling) but don't feel right taking the chance.
PGD seems so extravegant...and I don't want multiples so...hmmmm - not a clear path eh?
Good luck with your decision.