1) Please dont change $ZConfig['System']['system.chmod_dir'] = 0777; in config file as it is same i.e. 0777 when installed manually on cPanel also.
2) We have kept config.php bcoz it is required for upgrade from 1.3.x to 1.4.x. Kindly check upgrade process for 1.4.x to 1.4.x in next update and add it.
3) Table menu_items in not generated post upgrade from 1.4.x to 1.4.4 because menu module must be manually installed.(Confirmed with vendor)
4. PHP REQUIREMENT LINK : https://github.com/zikula/core/blob/1.5/INSTALL-Core1.x.md