That's interesting. There could be different ways to interpret the passages in the Instruction Guide, and it was so ambiguous that it could be interpreted in contradictory ways. It does seem that we do need to have completed the program, though apparently they seem to be under the impression that it is possible to complete a program, yet not obtaining any credentials upon its completion (the most confusing part).
All the same, we know that you only had 64 points without any adaptability points, so after the appeal, they must have given you at the very least another 3 points. The thing is, there is another user here (I believe it was beishidashuo) that appealed after his NER precisely due to the lack of 5 adaptability study points, and got PER as well, so it seems to me that the 5 points should be awarded for those who have completed two years of full-time study, regardless whether the program has been completed or not. And because they mentioned in the NER letter that they would not accept any new information, most likely you could not have done anything regarding your wife's education, so the extra points points must have come from previous study in Canada (whatever that really means).
If this was the case, then hopefully from now on, they would just automatically award the five points to all PhD stream applicants, so the new applicants won't have to go through the process of appealing, just because some officers interpret the instruction guide differently than some others.
Anyway, I should not hijack your happiness (or relief?) with my non-sensical rant and pedantry, so hearty congratulations once again
