When creating a Custom UI that doesn't have a menu but is more designed as an overlay such as a minimap, the left click and right click mouse events pass through to minecraft fine and you can place and destroy blocks as normal. The mousewheel however is blocked so you are unable to navigate through the hotbar items.

Not sure if this is an intended side effect or whether it's easier to add another parameter to the gui stack to just ignore all input events.

Can provide more detail if needed.