Looking back over the instructions I notice that you don’t need to match the top notch, just underarm and sides, but I don’t see that will make any difference. I wonder if the side notches were out because perhaps you sewed those other seams a bit low on one side or something? I’ve made this a few times and haven’t had trouble with this step. If I were to make it up I would match the underarm seams perfectly and then pin the underarm sections up half way so there is no gathering of the underarm section of the sleeve. Then I would gently gather the whole top/over shoulder section of the sleeve so it easily pins to the opening, spreading the gather evenly. You are not actually meant to see any gathers of course, it just eases the fabric in, so if you are a little bit out to one side it probably will make a big difference.