1.
ClrMamePro. IIRC, you need to set the emulator to "old_mame", but otherwise the same as upgrading old sets to new. (You'll still need to find any roms that were removed in new sets.)
2. Well,
FAQ. But more info: There are multiple chips per game, so you have a set of roms ("romset") for each game. (open the zip file, or check out
MAWS, and see the multiple roms.) If one rom was wrong (bad dump,
hacked repaired in from different version onto PCB dumped, etc), it should be corrected with new versions of mame. However, old versions of mame still want the
wrong rom. With the newer, more strict error check mame has on romsets, it's not as likely to have wrong roms as it was in the past, but it still happens; no one is prefect. (There still is the "not dumped yet, but now is" romset change, but that doesn't hamper backward compatibilities.)