Following from Tip #1, when you create your custom .dwp.  Do as little configuration as possible to the out of the box (OOTB) CQWP before exporting it.  I usually just add the OOTB CQWP to a page, then go into its appearance tab to update its web part title to  Contoso Content Query or PM Content Query before exporting it.  This way, when you add it back into the site collection’s web part gallery it’s as close to the original as possible.