Wanted to share an update. I think it's finally behaving really well! I've ridden it for a few days now and no issues. The last thing I did was replace the plugs on 2 and 3, fine-tuned the timing on 1 and 4 and found that timing on 2-3 was slightly off. I actually didn't know the Dyna S had adjustment for cylinders 2 and 3.
Thanks for everyone's assistance on this. I couldn't have done this by myself.