No you can only load the boot loader using a programmer connected to MISO, MOSI, SCK, SS and reset.
So if I was to pull the reset pin out of the schematic... Would the button still work?
Not sure what you mean by "pull the reset pin out of the schematic", but if you want the button to work it must be connected to the reset pin (30 on the 1280, 1 on the 328).
thanks for not flameing my n00bishness
No problem, we'll help if we can, but are you sure you have the experience to do this?
Truth is rather than seeing what you can take out of the Arduino circuit you may be better off looking at what you need to add to a bare chip to make it work (you don't need much actually) as it doesn't sound like you need much for your application.
I'm sure there's a a stack of "stand alone Arduino" threads here that can help.