If you take a look at the actual file, there are instructions there that might help you. You can create multiple zipship zones within the module. It is set to 3, but you can change that in the file itself. Try breaking up your zip codes into related areas and place them in their own zone see if that helps. Be sure to set your rate tables accordingly.
I built this for a very limited application and to be honest have not taken a look at it since. Its original intent was to create a small zone near my customer's brick and mortar shop that she would offer free and reduced shipping to based on order total.
As shipping module parameters are written to the configuration table in the database, the parameters are set for "text" in the db for the "value" field which is where zip code list is entered. There is not a specific limitation for that field set in the db, where the key does have a 255 limitation; however reducing the size of the zone might help you and help processing time.
Sorry I can't offer any more suggestions.
Ruth