Hi
SPI clock usage should not affect USB operation - if you use the IRC48 for USB clock generation you can be doubly sure that other clocks can't affect it too.
The links below show the FRDM-K22F used for composite USB as well as with SD card or SPI based Flash or SPI RF tranceiver (in parallel), which you could look at in case you prefer a complete and industrially proven solution to save development efforts.
Otherwise it would be helpful to known what software sources you are using presently so that someone can tell you what incompatibilities they may have between each other.
Regards
Mark
Kinetis: http://www.utasker.com/kinetis.html
K22: http://www.utasker.com/kinetis/FRDM-K22F.html / http://www.utasker.com/kinetis/TWR-K22F120M.html
For the complete "out-of-the-box" Kinetis experience and faster time to market
:smileyinfo: Out-of-the-box support for 46 Kinetis boards and 10 IDEs (460 combinations from a single code source with no porting required)