Congrats on the first long ride! The fjr is a fantastic bike for distance. That is one area of the country I have never been, but it is on the short list of places to get to!
I have a 2010 as well, and have done the same bar adjustments, and use the stock seat. As far as the shoulder issue, Skooter hit the nail on the head, read that and practice practice practice! Keep pressure on your feet, and be mindful of your torso body position. The reason your shoulders hurt is that you are using your arms to push you off of the bars. If you have to change your body position to take one hand off of the bars, then you don't have the yoda technique down. For me, adding a tank bag added to the awareness of this poor position. If my stomach touches the tank bag, I know I am not riding correctly. Also, I know I'm not riding correctly if my grip feels tight and my wrists feel heavy. I tend to ride with 2-3 fingers on the levers just to make sure I'm not gripping too tightly. It also feels natural to me as I grew up riding dirt and still do, and that is how I was trained(well, maybe not 2-3 fingers, but atleast 1-2). Anyways, pay attention to your grip and arms the rest of the technique will come naturally. Atleast it did for me. As Skooter said as well, the more you ride and the more long days you put in your body will build up to it just like it does anything else. Pretty soon 1,000+ days on the FJR won't feel like anything(except for maybe your butt, that is the one last thing I need to figure out, but a bead seat cover is good for 1,200 miles in 24 hours for me, haven't pushed it further than that yet).