LOVE wpuf ... it's one of my, if not THE, favorite plugins.
I've quite heavily customised three files "wpuf-dashboard", "wpuf-add-post" and "wpuf-edit-post". I've done it in ways which aren't 'doable' through the various action hooks, custom fields, etc. that you've provided. (I suspect if I could have, it would have been easier, and I'll spend hours working out how to do things 'the easy way' so it'll save me five minutes!)
Is there a way - perhaps an equivalent of a 'child' theme - to automatically retain these modifications when you release an upgrade? Or do I have to keep copies of those files separately and replace them after upgrading (or redo the modifications if you've changed those files in important ways).