It has the potential to be a good and fun project. I helped a friend this spring with such a project for his two sons. Each built their own mountain bike. One of the kids really seemed to enjoy the building process. The other could take it or leave it. All-in-all, we did have several enjoyable evenings.

BMX bikes tend to be simpler than mountain bikes. That works in your favor. If you do build w/your son, keep the sessions short. I found that attention and enthusiasm seemed to drop after an hour and a half or so.