I'm no expert. But I have been a "back yard mechanic" for almost 6 years, and I have already started a cafe project. On a bike you have three "sections," if you will. First is mechanical, which can be broken down into: air, fuel, mixture of air fuel, oil, compression, exhaust, spark, transmission, braking, etc. Then you have electrical, which is NOTHING compared to something like a computer build. Then you have cosmetic. In a word, cafes are cosmetic projects. (For the most part.)
The reason so many people talk about engines is because they want a perfect running bike, that happens to be 40-50-60 years old. Usually there's something wrong with them, even if it's minor. Another reason is performance. Cafes are in fact, racing bikes, even if they're not actually being raced (read up on history of cafes, there's a good YT series somewhere). In simple terms, if you don't feel confident in splitting the cases and replacing clutch plates or re-doing the top end, buy a GOOD working bike, and slowly learn new procedures.
With that being said, like I said earlier cosmetic is the biggest problem with these projects. I wouldn't be ANYWHERE without my grinder, drill, and jigsaw, and I still want to get several more power/table tools. A few questions you may encounter are: do I want a metal or fiberglass seat pan? Can I get the materials? Can I make this crap work? Do I have to buy tools for this? Does this look good? What's a cafe this, what's a cafe that? How in the hell do I get that off? How in the hell do I get this back on? Basically what I'm saying is cafes are more "crafting" projects. I've spent more time with Styrofoam and marker on my hands than I have with dirt and grease.
Of course, you could just buy a CB750 and get a few bolt-on custom parts. Everybody and their grandma makes cafe accessories for CBs and the bikes are dead reliable. Good luck finding one though...
In closing, the number one thing that will, and should be the VAST majority of your time, is looking at your bike in the shop. "Does that look good like that?" "Should that be lower?" "Should I paint that blue or gold?" I'll stand in front of my bike for up to an hour straight just looking at it and thinking about different ways something could look. In the words of Horacio Pagani: to achieve beauty, you must design every part so that they are beautiful in and of themselves, only then can you bring everything together.