So I finally imported my merged MAME set.
The "original" set is complete and on my server, so I will try to manually clean up the roms folder by comparing the audit list against the roms folder and we will see if I can manage to remove everthing without nuking a game the is in LB, and before that I can clean up LB since I won't be keeping most sports games, lightgun games, and other.
I know this is minor, but I wish there was an option to "Delete all non imported games" in the MAME import wizard, because if I'm skipping all the Majong games I don't really want them using up storage space.
Thanks for the help everyone, and if there is a third party tool that can accomplish what I am trying to do please let me know, and I've already got an idea how to add any required CHD to my list only for those games that require it.