Updated 02/11/2007: After finishing the initial non-destructive modification and being very happy with the results, I decided to mount the eSATA connector in a more permanent fashion.
Obviously all bets are off when it comes to warranty now.
So, I carved the security slot to fit the eSATA connector internally. This gives a cleaner overall look, and you don't have to worry about breaking off the eSATA connector if you are the type who moves your Mini around often.
Since I had both enclosures open again I added a newer, slightly larger hard disk as well as cleaned a few things up, including adding foil shielding to the exposed wiring on the internal SATA/eSATA cable, and reduced some of the excess wiring in the MiniStack enclosure and more securely mounted the MiniStacks' temperature probe to the bottom of the drive.
Original SATA/eSATA connector that was used.
Hacked up SATA cable. Exposed ends were later covered in hot glue, and wrapped in foil shielding.
Mac Mini with eSATA port.
Cleaned up MiniStack cabling. Added 320gb drive, attached heat sensor to bottom.
Finished. Warranty voided, but happy with the end result.