Bootloading ATMEGA32U4RC-MUR with Arduino Leonardo Recieves Error

Hi all,

In my original PCB design I called to use an ATMEGA32U4-MU. In the PCB I have it connected via SPI to an RTC, a SD card holder, and an accelerometer. In addition, I have connected a 16MHz crystal to the ATMEGA chip with two capacitors off of it to ground and a 1M ohm resistor connected to XTAL1 and 2 (just like in the arduino schematics for the Leonardo). I ended up having to buy an ATMEGA32U4RC-MUR due to availability of components. I put it on my pcb and have been trying to bootload it with an Arduino Leonardo but I keep getting:
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 1 of 10: not in sync: resp=0x03

I added a 10uF cap to ground on the reset line and redone all my connections and checked them and everything seems right. I am mainly trying to see if by using an ATMEGA chip with an internal calibrated RC and also connecting a 16MHz crystal if that will mess it up. If so what should I do?

Describe in detail how you connected the Arduino Leonardo to the custom board and what sketch you loaded on the Leonardo!