I'd fix it now too, definitely. I don't know how obvious it is in real life, but if it's this clear from that distance in a pic, I think it would stand out badly once painted. And that will be a highly visible area. Just my opinion.
At this point, I'd take it into a different area/room to do the work on it, to avoid adding more new dust into your paint area.
Curious, why single stage for jams and 2 stage for the rest? I don't know that I've ever heard of that before. I'd just use 2 stage for all of it. What's the reasoning there?