I'm surprised your script takes so long. 2MB is pretty large but I think I have a script that will work faster (I'm talking at most seconds, not a 1/3 of an hour). However, if you have many of these files it may ultimately be best to address this issue as a batch process outside of XMetaL Author.
Please try the scripting workaround provided as an MCR file located here:
http://forums.xmetal.com/index.php/topic,989