1. Have you read: Upgrading from PhreeBooks Release 2.1 and Lower http://www.phreesoft.com/?page_id=479
2. You should not have a problem here. Check your error logs for errors and post them here. If you use multi currency try turning off auto update and enter rates manually. cost price and full price will be in your home or default currency.
3. The best way is with a PO, but if you don't have to many items you can use Inventory Adjustments. Also have a look around in Tools> Import/Export