Using a ren command from .7z to .zip I was able to get MALA to populate the refreshed working game list. Once I changed it back everything works fine. I wasn't able to get Romlister working with this trick however.

Now the only issue I'm running into is how to add secondaries to the game list. Example, TMNT2p is inside the TMNT merged set and MALA won't automatically populate it. I'll likely have to go in and manually edit the list to get it added - or unmerge the set for games I need these on (a few SFs and all the 2p variants of my fav 4p games). Any thoughts on tackling that issue?
It's a bit easier for me right now as I'm working with an extremely limited list for my current build. 120ish games. I'll have to do it again once I start tackling racing games but that will also be a small list (less than 20 I imagine). If I was working with my full sets it would be enough to send me packing I imagine.
If you're wanting to work with small sets it's really easy if you build the lists in mame then use a rename utility to add the right file type to the rom name and a one line list copy script to grap them from the rom folder and move them to a new folder.