Got some more information,
I did the template debug on my life store and noticed there are two blocks the upgraded clone no longer displays.
One is block:
Block ID: 4649
Name: content_top
Controller: common/content_top
Path: storefront/controller/common/content_top.php
Template: storefront/view/bluestarway_theme/template/common/content_top.tpl
Parent: page
The other block is:
Block ID: 5549
Name: banner_block
Controller: blocks/banner_block
Path: extensions/banner_manager/storefront/controller/blocks/banner_block.php
Template: storefront/view/bluestarway_theme/template/blocks/banner_block/flex_slider_banner_block.tpl
Parent: content_top
I went to Design -> Layout and the 'home page slide' block is still active in the 'Content Top' block holder
For the super menu, both life and upgraded clone show same number of blocks, however upgraded clone doesn't display the super menu.
NOTE: I'm using a template clone of the default AbanteCart cart template. Maybe some files I changed in my template clone? I know I did slowed down the banner rotation time.