At the moment we have quite a few script files and the only way we were able to get GWT and our product to work together is by adding all imports manually into the HTML file (which forces them to be loaded before GWT).
Could you please explain why this is the only way they will work? What happens when you use "<script src=.../>" tag in your module.gwt.xml?
At first glance, I assume that your scripts must require that certain page elements already be available before they run. In that case, you could try loading them in the module via the gwt.xml file, then use a very simple JSNI method from your onModuleLoad() to initialize the scripts. This way your scripts could be placed into the page at load, but only triggered when GWT was ready for them.
Hope that helps.
Sincerely,
Joseph