Always build the bike that stirs your soul regardless of others opinion. But, some input on your statements:
- You find the stock riding position and bars to kill your shoulder blades after quite a few miles.
If you have not ridden a CB with rearsets and clip-ons yet, then you are in for a major disappointment. They will be far less comfortable than your current setup. It will be more fun for about 20 minutes, but after 100 miles, you'll be screaming in agony if the current stock config is hard on you.
Rearsets moved back a bit, and lower, can actually improve not only your comfort, but actually improve your technical handling of the bike. Yours are positioned a bit far back, but only time will tell.
Superbike bars, Euro bars or something more "upright" than clip-ons will improve your comfort. Torso up, feet low and slightly back, is the best posture for long riding. You could use clip-ons with higher risers as a great compromise on styling and handling/comfort.
Here's a picture as an example.
Whether you buy or build a seat, don't skimp on comfort. I'm not encouraging a vintage King/Queen blue vinyl abortion from the '70s, but a nicely crafted and gel-padded slim seat is a great addition. It wants to have a slight "crown" in the middle to fit your body's ergonomics. You might investigate the stock pan with a better molder pan and cover to suit your design and comfort goals.
Something that is "trending" due to meeting all the objectives listed above is "street trackers". These bikes ergonomically address the items listed above. Very often the builder cites: "I wanted to build a bike that was actually comfortable to ride, and not just cool to look at."
That admission says volumes to me. So if this will be a heavily used, long term ownership bike, give some thought to these ideas. Better yet, go ride some new bikes in differing styles and decide what about each you like. The bars are comfy, the seat is nice, the pegs fit me... Then use these fitting measurements to build the bike tailored to you, for you. And that, we will all applaud and get behind!
Hope this helps, and doesn't infer any offense.