With modern electronically controlled fuel injected engines there really is no such thing as a "tune up" in the sense there once was when engines had carbs etc. That said, the things the manual does not mention that you can also consider include cleaning the MAF sensor (do a search on this forum for how to do it) and possibly running something like Seafoam through it - but 40k is pretty early for something like that unless you have been experiencing poor performance etc.