...
One problem you will encounter is that during boot up the serial port(s) are used by the Arduino to check with the IDE.
D
Hmmm. How do you get around this?
Wait, here is an idea. You could have one Arduino power on the second Arduino using a TIP120 transistor.
So, first Arduino boots, doesn't see the IDE, starts the second Arduino. The first Arduino resolutely ignores any activity on the serial port until the second Arduino boots.
Also, once the code is sorted out, you could use AVRStudio to transfer the software without the bootloader.