that's a loaded question! It all depends upon your budget, tastes, skills and goals. There is an unlimited level of upgrades and modifications available and undertaken by bike owners. If you can think it up, it's probably documented somewhere on this forum.
Suspension upgrades range from new springs or cartridges in stock forks, to swapping to GL forks, to swapping to modern sport bike front ends.
There are numerous cafe seat and tank builders, either in fiberglass, carbon fiber, aluminum or metal. Exhausts are other changes that owners make, and rear shocks. Modern clocks and gauges are also available.
The best place to start is the internet. Google CB750 cafe racers (if you're determined on that direction) and browse pics and build threads. Gather you're ideas, then decide upon "build it or buy it". There's a ton of gorgeous builds on this forum by some embers here for the 750. Tweakin's latest build comes to mind immediately. There's numerous 550 builds from: FunJimmy, Bru-Tom, Hannibal, and CB750's recently completed 750. It's all there for your viewing pleasure. Most of these guys documented fully their process or vendor choices.
You just gotta read and choose. Or go your own way and start a thread. Many will pipe in with great advice and caveats. First and formost, get a copy of Hondaman's book, it's an exceptionally written documented guide on the Do's and Dont's on these bikes.
Hope this helps a little...