it is not possible to upgrade from 3.x to 4.x a fresh installation is required.
the paths are the same, the partition was added to be able to handle the sd files in windows, eeroms is a storage / roms symlink.
the log seems to be related to AdvancedMame, try switching emulator / core. per game (holding button to launch game / game options / emulator.)
globally (in game settings / advanced settings by emulator / mame / emulator
What is the version of MAME core?
Different MAME version may change the required ROMset.
If MAME core is newer in EmuELEC 4.3, the required ROMset may also need update.
you are right, it depends on the romset you are using; probably the latest AdvancedMame version will work fine for you, if you want you can try the released beta 4.4 but keep in mind that it is in the testing phase