I have been very careful not to break existing skins during upgrades and in cases where some change is needed I note them in the Important Skin Changes article.
Our extraskins.zip (on our codeplex download page) has skins from older versions of Artisteer going back to version 2, 2.4, 3, and 3.1 and all of those skins still work correctly with the latest version of mojoPortal even though the markup and css for Artisteer has changed a lot over those versions.
I have never offered any support for changes made to the Artisteer designs or exported css outside of Artisteer. Your skin has modifications to the Artisteer css, additional things from some grid framework, and superfish, and hard coded styles and tables used for layout inside the content. All of these things introduce variables beyond what I can offer support for or forsee the impact of during upgrades.
The safest course of action is to always upgrade a local copy of a site first to evaluate any possible problems before upgrading the production site.