Try using the Easy Transfer
tool, if the old OS is still installed.
Programs cannot be transferred; you must reinstall them on the new OS.
You favorites are stored in your user folder, so in Windows.old, you can find them in C:\Windows.old\Users\[username]\Favorites
When you have copied all you want over, it is safe to delete Windows.old: Windows.old Folder - Delete
On a 64-bit system, there are 2 program files folders: one for 32-bit programs (Program Files (x86)), and one for native 64-bit programs. That is normal, and helps keep track of your programs better.
You can choose to install a program anywhere you want; those folders are just to help keep things organized.