The problem that you are experiencing regarding the top padding is related to the custom CSS that you added into X > Theme Options > CSS.
You added a 0 height to the header and it ruins all the calculations of the Fixed Top feature of the header of the theme:
There might be other problematic code chunks there also.
Please kindly consider that we do not support customization related request, whether it is the customization itself or a side effect of custom code that you added to the theme. You will need to contact a developer to implement the customization or fix the side effect for you.
Thank you for your understanding.