Growing up I always went trick or treating just the same as my siblings. After trick or treating was over I simply traded the candy I could not eat with my non PKU siblings for candy that I could have. This worked perfectly for my family, because my brother and sisters were always more than happy to take all of the chocolate off my hands, and I loved getting candy that I could actually eat. In fact most of the time we made it into a game in which my siblings tried to 'one-up' each other by offering me the candy that they knew I liked best to get what they wanted. This is what we have continued to do with my thirteen and three year old sisters who also have PKU, and it has worked wonderfully.
If Jacob's sisters are not trick or treating when he is old enough to start you could purchase candy from the store. It would be the same concept, except instead of trading with his sisters he would swap his candy with the PKU friendly candy you bought. Other people I know purchase small toys and trinkets, and their little one can 'buy' the toys by giving over a couple of pieces of chocolate for each toy.
If you want to do something else and take the focus of Halloween off of food though that is perfectly fine to, and ultimately it is your family's decision how you want to handle Halloween and Jacob's PKU. I can tell you though that although my trick or treating experience was a little bit different than other children I never felt deprived or like I was missing out on anything. I got to dress up, walk door to door, and enjoy my treats afterward just like any other child.
As for school parties my mom always kept a small container of PKU friendly snacks at my school. My teachers usually kept it in one of their cabinets or the teachers lounge, and when we had parties if there was something I could not have I simply picked a treat from my 'treat box.' However, most of the time teachers will tell you when class parties are being held ahead of time, and you can plan to send low protein cupcakes, cookies, etc on that day. Again, for me this was never an issue. As long as I got a treat as well and it was something I liked I was happy.