atmega328 not accepting code(please help using bootdrive)

Hi guys!So I have an uno bootloaded standalone atmega328p on a breadboard with a seperate micro usb power supply.I also have an arduino uno rev.3(atmega328 based).I am trying to get the uno to program the standalone atmega328 using a program from an sd card.I am using bald wisdoms bootDrive to do this:http://baldwisdom.com/bootdrive/

Ok so i have the setup, and put the .hex file into the sd card.When i try it,the standalone atmega is receiving something(pin 13 flashes rapidly),but it isn't running anything. :o Bald Wisdom's pinout for bootdrive is super COMPLICATED.It only requires 3 pins,but n the code he has one set of pins,on the website he has one set of pins,and on the diagram on his site he has a different set of pins.In the video(on his site)he says that pins 4 and 5 on the I2SD are pins 1 and 2 on the uno.When i tried this it still didn't work.Here is his code that I'm using(the forum isn't ;etting me post the code because it has to many characters)What should I change the variable #define BOOT_BAUD to?I put 9600 but it was 115200 before.Which pins should I use?By the way what does it mean by indicator leds on pins 2 and 3 in the code?Here is the code link:https://github.com/osbock/Baldwisdom/blob/master/BootDrive/BootDrive.ino