I think that spending in Europe also tends to be skewed towards large undertakings (at least this is the case in Germany where the automobile sector accounts for over half of all private sector R&D), whereas the largest potential for wealth creation lies in R&D by SMEs.
Maybe it's silly to speak of a 'gap'. In terms the economy at large, it is probably better to spend quite a lot on fundamental research, applied research and the development of technology as it is one of the most potent sources for the creation of wealth.
Caveats with regard to creating wealth apply, though I think that changes in technology is a potent force for the betterment of just about anything. If used wisely...
I have no idea what would be behind the Japanese figure, but I'd be interested in the structure of it.
Problem solved.
The difference in private sector spending points at something real. Of course, the figures need to be broken down, as you indicate. It may be that in the case of the US it is merely spending on military development and patent trolling. That's an interesting topic for further research.
I think that there is a fairly continuous line from fundamental research to applied research to new product development, and therefore it makes sense to group them together when doing an analysis in an economic context.