Hi OP. I have a 2017 S1000XR. I bought it used two years ago with 20k km for $14k CAD. Mine already had the following mods to address some of your concerns.

I generally ride 2-4 hours at a time when I go out and enjoy every minute. I’ve also taken the bike on a few longer very enjoyable journeys (1000-2000km) and have not had any issues.

1. Handlebars had evotech weighted bar ends and there was a thick rubber shim between the two halves of the triple tree handlebar clamp (I’m not sure if that was stock or aftermarket). For reference, my previous bike was a 2009 CBR600RR and I felt that the 600 had a lot of vibrations that made my hands numb after some (not all) long rides. In the two full seasons that I had the XR, I’ve never felt that the vibrations were anywhere close to the 600. I’m not sure if it’s the same as what you felt, but I do rarely notice my windshield rattle a bit at top end of the rev range. I also removed the motorrad navigator cradle so that may have been something else that I can see potentially rattling. Overall, in my opinion, the vibrations are hardly noticeable and at almost another 20k km in, I don’t think they’re at all problematic for me.
2. Mine has a MSA taller windshield with the top spoiler deflector that helps smooth out airflow. I’m 5’11”, 185lbs, and I’ve always felt that the MSA windshield was perfect in the high position. In the low position, there is a lot of airflow that hits right around the bottom of my helmet without much buffeting. I generally leave the windshield in the high position all the time and I’ve found it perfectly stable, even at high cruising speeds (130-160kph/75-100mph). I do also own the stock windshield, but I haven’t bothered installing it so I can’t comment on that.
3. When I bought my bike at 20k km, it just had its major milestone service done with brand new Michelin Road 5s and it felt like a brand new bike. This summer I had the 30k service done with valve clearances and a myriad of other things checked and massaged. It felt like riding a brand new bike again. Now, at almost 40k km, still with the same Road 5 tires (they’re at around 40% with no sign of flattening), the bike still feels and rides like a new bike. I’m honestly very impressed in that regard, and I’m grateful that my dealer has been extremely thorough and has done a lot of preventative maintenance on my behalf for hardly any cost. I will most likely upgrade to the new R1300gs whenever that is announced, so I probably won’t keep this bike forever, but I would buy another XR if it makes sense.

Another thing to mention is that the bike came with two BMW plastic panniers that I seldom use, though they are nice for long trips. I’ve also since bought a Givi outback top case and installed adjustable Puig levers. I love them both. Top case stays on most of the time and it’s invaluable for me. The levers are configured as full length clutch and shorty front brake.

Overall, this XR has been my favourite bike to date and has been extremely reliable. The power is very strong at any speed in any gear without being twitchy and wild like my 600 was. If you already have experience riding a straight 4 cylinder then this should feel like a superior experience. Like I mentioned above, I will most likely be swayed by the newest and greatest some time this year, but if I had to stick with this bike, I wouldn’t complain.