To play backups and retails on your XDK, be sure to grab Hack-devkit-GueuX-V2. It's in the usual places and it is very easy to apply.
Yes, if you decide to open the unit, you can swap the dvd drive without any concerns.
As far as the larger HD is concerned, I believe your best bet to run a debug BFM bios with LBA48 support. I'm not quite sure on that one, so could some one verify this?
It would be a shame to brake the seals on your mint XDK, but if you don't plan on reselling it, then why not

I have a debug Kit with Kernel 5335 and when i applied the Hack-devkit-GueuX-V2, all i get is garbage on screen. I can see that it did get to the debug launch screen but the screen is flickering. U think that this could be due to the xboxrom.bin?