I breastfed my daughter, Isla (now 2 and a half) until she was 10 months old (which was when I went back to work). I had to give her the formula on its own for about three days and then reintroduced the breast milk. I pumped for the three days she was just on the formula, then I would just give 30mls formula before each feed, and let her nurse until she was full (sounds similar to your regime, I am based in the UK and we did not have to express / measure out the breast milk, I think it was just guess work!).
I did most of the bottle feeding as well as the breast feeding, as I was on maternity leave and my husband had to work, and Isla didn't get confused, she just adapted! I was so pleased I was able to carry on breastfeeding as I was also really upset at the thought of not being able to do it. I never really did much pumping except for those first three days, and I found that my body just started to produce the right amount of milk. I suppose we were lucky that we had found breastfeeding quite easy in that first week, and then we just adapted to the bottles fairly quickly.
I know the diagnosis is a shock but I really regret the fact that I did not take time to enjoy my first few weeks with Isla (I even refused to open our baby congratulations cards for a few days after the diagnosis because I guess I was grieving about not having a perfect baby) – now I can't see why I wouldn't have wanted to celebrate my beautiful daughter because she is such a blessing. So I guess I just mean take time to enjoy your son and not think too much about the PKU, it will just become a normal part of life.