FYI, I think the mod system is broken right now if 2 mod's modify the same file. I've been too lazy to test and report it, but I found that regardless of order, the last mod doesn't modify the result of the prior mod, but instead starts from the backup copy of the file all over, thus wiping out the prior mod's changes entirely.
Thus why right now it has to be end of the loading order, as my random portrait mod also modifies mainmenu.gd, but then this means your mod being at the end of the order is almost definitely wiping out my mod's changes to the file.
The bit I modify in mainmenu.gd is tiny though and not critical to the random portraits mod working. It was primarily a fix to have it re-choose portrait for starting slave after you customize them.
Any other mods though that modify any of the similar files will likely not play nice, even though you coded it to try and play nice as much as possible :(