Thanks for the feedback CrossRoads. I've updated the schematic with the 22R D+ & D- resistor values as well as changing the 10K i2c pullup values to 4.7K.
I've read that others have overclocked the 32u4 @ 16Mhz with good results. The only reason i'm doing this is because I use the default Leonardo bootloader and program blank chips using the USBtinyISP. If I ever figure out how to tweak the frequency then I'll give it a try along with a modified PID/VID.
About the SPI SS line. Right now SPI only talks to the SD card. Should the SD_CARD_CS line on the SD card holder be connected to the 32u4 pin 8 PB0(SS/PCINT0) ? Right now I can read and write to the SD card so I must have the SS line configured as an output.
S2 is just a simple pushbutton so I have the 10K pull down as used in all the simple button examples. http://arduino.cc/en/tutorial/button