I went through this when I set up my factory EFI on my 1999 OBD2 system, and used the pre-cat sensor for the closed loop metering.
I also hooked up an electronic cat simulator to feed an artificial post-cat signal to the computer to not have it throw a code and go into limp mode. However, I'm not sure not having that signal would have thrown it into limp mode. It may have just turned on the check engine light and continued to run as programmed.
You can always call SOLO PCMs in Florida, which is where I got my ECM with no security and set-up for a manual trans car, as I run a 2004R. Another great resource for SCT Tuner custom programming is Chris at Performance Injection Equipment.
