Yeah, and if you want a better, non-screwedup bootloader, that has the ability to write flash (Only tested on the 2560) go here:
https://github.com/xxxajk/Arduino-stk500v2-bootloader
I still need to write the...
Pin assignment doesn't matter on the host, only the target really matters.
Here's a starting point for you, that uploads a bootloader, it's pretty easy to modify to upload program only....
Yes, this is totally possible.
I have a similar set of tools that I have made for mass programming.
The bigger question is are you wanting to burn a bootloader, program only, or both?
For program only, with a...