According to the old wiki, the first bit of code you can change is the GPIO config using the output of a tool called inteltool. However, it states that the config is in mainboard.c, but in the case of the T400 code, it was moved to the gpio.c file.

Looking at the code initially, I could figure out how the configuration file was set up and what each line did, but I could not correlate the hexadecimal output of inteltool with the lines of code. Upon closer inspection, I realized that each binary bit in the hex numbers corresponded to a certain GPIO pin that could be configured. The value of each bit position indicated things such as whether it was used as a GPIO, signal direction, output state, and inverted inputs . Soon I had the file edited to match the GPIO config for the E6400.

I later found this information somewhere on the web, but by then I had already figured it out.

I did try flashing it after this, (and I had to desolder the chip, as it seems that using a SOIC-8 clip to to ISP may be activating other parts on the board and interfering with the SPI communications) and unsurprisingly, it did not boot. More work still needs to be done.