It's been a few months, so I figure I'll share my non-progress. I haven't touched the car in a few months. It runs very well except I'm still fighting the IMRC delete issues. My solution of physically removing the IMRC but leaving the flag set to "1" (enabled) in the computer eventually threw a code saying the IMRC wasn't functioning, and my tune went to crap again.
To get around that issue, the IMRC is wired/hosed in, just not actually attached to the IM. So far I'm wishing I would have not gone with that Cossie style manifold. Overall though I'm quite happy with the build.
I'm not sure 2013 will result in a built motor at the moment. Instead I'm looking to put money into the house instead of the car.
'04 Mach 1. Built. Turbo. 667whp/631wtq
'06 Focus. Built. Turbo. WMI. (sold)
'03 Mach 1 : 12.61 @ 106.59 (sold)