The Lund kit I did we ended up putting the pcm behind the front bumper. The fuse box can be mounted at an angle to clear the passenger side turbo or relocated entirely like the above link.
man you did such a good job with all of that. i always go back and look at the pics. one day i will get the motivation to do the same. in june i will be on leave for 30 days and will get bored. maybe that will be a good time to take on this project.