Hi Pat C,
Like some other folks here, I came to the FJR from a cruiser type bike, big, heavy, floorboards, bags, chrome, and all of 74 horsepower. That was 3 years ago (& 37k miles).
What I remember is:
1) Took me awhile to not grip the handles with the 'grip of death'
2) Bike was new, bars vibrated. 10k, vibration quite a bit less. 20k, yeah I think I feel some vibration. Now I Have to think about it to notice. I put on some heavy bar ends on at 7k, but I think the vibes just get weaker as the bike gets broken in.
3) SS1K was murder on the stock seat (for me, YMMV). Took Bounce's advice & got a Russell seat, best money I ever spent. 6/7/8/900 mile days can be done with very little bun fatigue.
4) The first week I had the bike (800 miles) I got sore in lots of funny places. Since then, no problem.
5) The Yoda position thing, while not exactly right for me, did help me attain my Zen position for LD rides.
I think you're seeing a little 'break-in' like I had.
All the best, enjoy the bike, & take an Ibuprofen before the long rides, it'll help.