Generally, for major upgrades, Jive PS will re-implement custom themes, rather than upgrade them, due to the large number of architectural changes that take place from major version to major version. The amounts to re-imagining the theme as it pertains to the UI in the new version, and implementing accordingly. Unfortunately, there is no easy answer for this.
Of course, the preferred method for making light modifications to your instance is with Jive's Theme Tool, which provides for upgrade-safe UI changes. While it can address many styling needs, it will not facilitate the adding of UI elements to the page. It may be a good idea to revisit your requirements to see if they can be pared down to fit into the capabilities of the Theme Tool.
Hope this helps!