Put the last finishing touches on the plugin and fix the most obvious bugs. Some I've noticed two weeks ago:

• Menu items sometimes don't stay at their position and get added to the end
• Custom menu items sometimes disappear
• Slugs/Links sometimes change (e.g. with the Email Subscribers plugin)
• When moving a top-level menu item, the first sub level item might be moved instead

After that, create a 2.0.0 Beta 1 release here on GitHub an perhaps even upload it to the WordPress.org plugin directory (but keep the stable tag at 1.0.1).