Here's hopefully a simple request: Since you can quickly generate a list of the .var files, and you can very quickly generate a list of the .var file *contents*...
Could you output a text file that is like cmd> Tree that lets us dump it into excel and list every single file in every single var?
From here, we can use excel to compare a similar list of our vam/custom contents, (IN PARTICULAR, MORPHS!)
From here we can look for duplicate morphs, which seem to be one of the most significant things to slow down the app.