The first thing I would do is check all fasteners for correct torque, paying special attention to engine and frame mounting bolts.
Bar end weights are sized by the manufacturer to reduce vibes in the rev range they expect most users of that bike will ride in. Using bigger weights will not necessarily reduce vibes in the range you normally ride at. They might make it better, or worse, or just move the smooth spot (Ninja 250's have more than one) around a little in the rpm range. The 250's are a lot smoother than most parellel twins. The 500 and 650's are way worse..the 500 not nearly as raspy as the 06, 07, 08 and maybe 09 650's. At one point, the 650's had some additional vibration reduction efforts..I think Kawi rubber mounted one end of the engine and that can help a lot. BMW parellel twins have a lot of unpleasant vibes also.
One thing I would suggest is if you try cruising at different revs and finding that smoother rpm. Then either shift up or down a gear to try to compensate. Naturally if you are doing faster highway speeds and find that if you shift down into 5th, then revs are going to scream up depending on how fast you are going, so not always an option. My point though is to experiment a little. If you find a sweet spot rev, then try swapping bar weights (both bigger and smaller...borrow from friends?) until you find a weight that inhances that sweet spot. It is easier typed than done though, as removing bar end weights can be a real pain as they usually are factory lock-tighten with red or blue (requiring hear to remove) and is hard to get to. I would try it on a hot day and place a black leather jacket or even a black pail over the bar end fort awhile so the sun can really warm it up. Then when you try to remove, keep a firm but slow pressure on the socket. This allows the loc-tite to break its bond slowly, and helps avoid bolts twisting off. You really don't wanna do that.
IMO, not enough emphasis is put on reducing vibes (that hurt) on bikes. People would not buy cars whose steering wheel put their hands to sleep, so why do we tolerate it on bikes? It is why riders will often choose a V4, or flat 4 or flat 6 or some other configuration with the engine rubber mounted. But rubber mounbing an engine is not easy to do and retain chassis ridgidity as they are used as a stressed member in the frame. It can be done in bikes, but cost is always a factor and mfrs opt for easy outs that are often not very effective, like bar-end weights and internal counter-balancing. They help, but night and day differences are rare. One tho comes to mind where that isn't the case..Kawi's ZX14. Smoothest large inline 4 I've felt.
Also try some aftermkt grips...ones designed, or have a reputation for addressing vibes. Also get some gloves that have gel in the palms. Grips and the gel gloves help quite a lot. First I would do though is confirm every bolt is torqued right, and some are hard to see without removing plastic, so the one you ignore could be the culprit. Good luck.
