What does your modified GraphML file look like? (See How to upload files to yEd Q&A? for upload instructions.) If yEd crashes, I bet your modified file is no longer GraphML but some Excel format. In any case, when reporting an error, please always include the error message.
When you mentioned a "vb script" it was not clear to me that you actually meant Visual Basic for Applications (which is usually abbreviated VBA). I doubt Excel is a good choice for text processing (which is waht step 4 is all about). I recommend using a stand-alone scripting language. The most natural choice would probably be PERL, but any decent scripting language will do.
