Abramz,
As I understand this subject the parts are generally made to bolt up to the stock locations, mixing and matching bike parts is just like the automotive world.
As an example you can buy an edlebrock intake manifold bolt it to a pair of Air research heads and throw on a demon carb to top it all off.
There are certain parameters but generally speaking it will bolt all together.
You can throw a lectron carb, kibblewhite stainless valves, titanium springs and a hot cams cam, on your bike with a leo Vince header, a Ti FMF megabomb midpipe and pro crcuit silencer and it should all bolt together with minimum "tweaking"
This might run like a crf 150....however it should all bolt together in the stock Honda Mounting locations...
Tuck\o/