UPDATE: Out Of Province Inspection and Fork Seals taking longer then expected. Oh well, we got a dump of snow, so its not like I could bring it home, even if I wanted to! :P
Step 1: Reasoning For a Simpler, Toned-Down Builds
Reasoning for not doing a true to the name Cafe Racer build was the low kilometers. If you bikes engine is in really good health (everything factory spec, good compression, etc) I suggest not putting on pod filters. Pods require re-jetting carbs, not a problem usually (although there are some bikes its impossible to run pods on, the carbs just won't jet properly), but they DO NOT filter as well. If you have a bike that is super duper, pods will gnaw away at the compression quickly. Pods do reduce the life expectancy of an engine, fact. With an engine with 1500km on it, I would not pod it since its a good bike and could last a VERY long time. As well, the airbox could only be removed if the engine was taken out (Which it was), but this makes for very difficult swaps to change it back and forth from pods to the airbox.
Another reason for the toned down build on my bike was if I am doing it up, but I still want to ride it a lot, I don't want it getting dirty so I decided to leave the rear fender on. Some Cafe bikes do have fenders, usually retro chrome ones, not cheap black plastic like mine. My fender came in 2 pieces, so the part that sticks out the back and holds the license plate came off and I left only the fairly well hidden inner half that would keep the engine from getting too much muck on it. If the fender on a bike is one piece, it could be cut and modified to have only part inside the frame to keep things clean without a big ugly black fender sticking out the back of the bike.
After going through decisions like this, I decided to do a Cafe Racer styled bike, but not true to the Cafe name. Essentially, making a true Cafe bike just requires removing more stuff that isn't 100% necessary for the bike to run and be legal and swapping out big ugly stock factory parts, like the airbox, with smaller/sleeker aftermarket parts, like pod filters.
Now I am not saying that don't do a full on Cafe build, but if you are, don't pick the bike that is like new, picking something with more kilometers, had its break in phase and won't suffer from some of the problems that a really super low mileage bike may. And be mindful of what complications some mods bring. As well, be weary or super low mileage bikes, sitting generally isn't good and you can easily get a money pit if you buy a bike with very low mileage that is old.
UPDATE: I am highly against Pod filters truthfully. They look good, I give them that, but are a pain. On XJ bikes, if you install pods you will HAVE TO re-jet, then re-jet again, fiddle and re-jet again, try syncing the carbs and re-jetting again, then try re-jetting again, and re-jet again...I think you get where its going. Pods can be a huge hassle on some bikes, and XJ carbs are too fiddly to have them installed (Although, some people have done it successfully). Its good to Google your bike and research its quirks as well.
The other thing I have against pods is that on cars anyhow, pods will 99% of the time give you no improvement or actually reduce performance. The engineers knew what they were doing with air-boxes, my suggestion is leaving them installed unless you know that pods can be fitted easily to your bike, don;t plan to do tons of riding, and you are in a dry, clean (not dusty) environment.