Restoring your iPhone from the backup for your wife's iPhone will not restore your contacts.
You should have restored your iPhone with iTunes from your iPhone's backup - the backup for iPhone at that time. There is a new backup for your iPhone now so you need to restore from the backup dated at that time.
Each iPhone can have its own sync preferences with iTunes. You can select the apps you want installed on your iPhone under the Apps tab for your iPhone sync preferences with iTunes, and your wife can do the same under the Apps tab for her iPhone sync preferences with iTunes.
Regarding contacts, contacts are designed to be synced with a supported address book application on your computer. Are your contacts available in an address book app on your computer, or you are depending on your iPhone alone for this data which can be lost or stolen?