Here's a different opinion I received from Empirical Audio;
The problem with modding the iTransport is that is uses the PCM270X chip from TI. This chip, even with the best clock on the planet is very jittery. I should know, I had products based on it years ago. The AirPort Express uses it also.
The best mod for an iTransport is no mod at all. Add an external reclocker like the Pace-Car 2. This will outperfrom by a long shot any mod that you care to do to it. Also, once you put money into mods, the mods become worthless. You never get your money out of them. The Pace-Car on the other hand has a great resale and lasts maybe a day on Audiogon.