No problems, tt. IC stacking is inherently less reliable than the other two approaches to the Hack. It's not like you're going to find a straight pin-for pin solution anyway. You have to have a mess of wires to do the conversion located somewhere! I like my messes of wire etched on PCBs, others have no problem splicing wires and hacking into connectors. I try to avoid that stuff like the plague. It's all a matter of what makes a hacker comfortable or uncomfortable.
After grinding or nipping all the legs off the original Controller IIC, desoldering each pin individually should be a piece of cake.
Soldering wires down in that crevasse to the Controller Chip's legs is what gives me the heebie-jeebies. The point of the PCB/header hack is the creation of a robust, reliable, detachable connection. The header is slightly cantilevered over the back row of pins, but the PCB should be solid as a rock the way I have it soldered to the MoBo. I don't foresee any problems cycling that connection a couple of hundred times, which would be a LOT. Better to detach the cable from the HDD, but avoiding that mess of wires without strain relief is to be avoided at all costs, IMHO.
But don't go by me, I'm b@^$#!^crazy! :lol:
edit: nice pics you've just added, there's only one problem, to do those mods you have complete, unobstructed access to the Arduino from every conceivable angle. :-/