After further help from Rob Dunsmuir of Custom Coding, version 0.99 of the Square Hebrew-Simulator is now up and running and available for public use.
This version correctly converts the ḥolam malé and shuruq in Square Hebrew to o and u, respectively in the Simulated Hebrew rendition of the text. Currently, the o and u are converted to undotted vavs in Square Hebrew—which is fine, but conversion back to ḥolam malé and shuruq is the next, and (we hope) final step.
SimHebrew is the first computerised converter of traditional Square Hebrew text into Roman characters and back again with full fidelity. For more details, see Introducing SimHebrew: Hebrew unbound.