Good afternoon Neil,
Widget management is greatly improved in Hoop.la 2.0, first the management tools for widgets no longer appear by default when viewing a page. If you can manage widgets then you should see a "Manage Widgets On X Pages" link at the top of the widgets in the right column. Example:
Once you click that link then the rest of the page should gray out and the widgets on that page will enter a "edit mode" which is much more condensed and makes re-ordering / managing the widgets much simpler. Once you are done managing the widgets you can then exit management mode and you should be good to go. This should help you with both of your first two points.
Next, Custom Widgets have always been a tricky animal. Due to how we would allow them to be created during the addition process for a widget on any page customers often had difficulty trying to edit the code within the widgets, or if they created it with broken HTML often they would need to go to a different section of the site to edit the widget to fix the problem. With Hoop.la 2.0 we decided to formalize the custom widgets as a full feature. They are now managed in the control panel at:
CP -> Design -> Manage Widgets
The landing page there is for Custom Widgets. From here you can create, edit and delete all of the custom widgets on your site. Once its created in that control panel you will then be able to select that custom widget whenever you are managing widgets on other pages.
Hope this helps, let me know if you have any further questions or if I can go into more detail about any of this.