Z - not to go too far on you but, you do realize every modification you are making is actually increasing the felt vibration, right?
I'm all for an aesthetic, ie vintage tires. But they aren't as generous with absorbing bumps. While your cafe seat may be pretty comfy, if it's hard mounted to the hoop, guess what? More vibration. And lastly, clip-ons. For rider comfort, they are the worst.
Don't get me wrong- I dig cafe bikes. I have clip-ons on my bikes. BUT, for traffic commuting on long bumpy roads, a sport bike bar, a naked bar will be much more comfortable and compassionate.
Just understand these aspects so that you decide if the money you spend is actually addressing the problem. From the list suggested, I see it very clearly getting worse, not better.