First of all, check if your root category is assigned to certain web-site and then under this root category you will be able to built-up correct category tree.
Also after that do not forget about flushing cache and doing re-index.
Read also this article on what should be checked -
As for products, they should be assigned to certain categories to be visible at the front-end. Also check their visibility, stock level, status. Get more details here -
If you will need to change any of the mentioned product parameters in bulk, you can use 14-day free version Store Manager for Magento application, as it has Multi_editor tool for bulk changes. Give it a fry -