@nitrogen_widget, Is there a reason you're using the older Pi models instead of upgrading?
I was looking at doing something similar to what CRTPi-RGB is doing, which uses a list of roms to determine the proper resolutions to set.
However, I liked the approach that CRT SwitchRes uses better, which is built into RetroArch. It uses the resolutions from the ROMs themselves to set resolution, refresh rate, and pixel clock. I got that setup working for my arcade last week.