Your problem definitely lies within the codes folder. I swapped my code folder with yours and the problem disappeared. I have attached my .gct and the codes included in it, (test to confirm). I suspect you're either using a P:M version of a code when you shouldn't be, including a P:M fragment that's dependent on other codes, or including a code that is incompatible with the Brawlex elements. Unfortunately this means further code trial and error on your end but at least I was able to narrow your search.
Also, can I submit the files you sent me to Dolphin's issue tracker? Your setup is one of the rare cases where Dolphin does not crash where the Wii does. We're interested in investigating those problems.
The .gct that does not cause your problem:
http://www.mediafire.com/download/56lwfe5ly4ycp93/Troubleshooting+PT+KO+CRASH.rar