Emulator rules for the EarthBound speedrun (and therefore this speedrun) are based on speedrunslive's rules for emulation. bsnes, snes9x 1.53, snesgt (the one i use), and vc are all allowed. Zsnes and all other versions of snes9x are banned, pretty much for the reasons you already listed.
Edit: But I guess it would do us well to specify that in the rules of the run as well so there's no confusion. ;p

Spotted this whilst searching for the game. It fixes the crash, and works on FCEUX.
To download, scroll down.
http://acmlm.kafuka.org/board/thread.php?id=7713

http://www.romhacking.net/translations/3388/

Made it quickly in photoshop, tried to make it look like the start screen.
https://i.imgur.com/rxJsDke.png

EarthBound: The Halloween Hack

Bio Hazard

New logo

English Patch

Crash fix