A P1000 means testing incomplete. The truck needs to be driven to clear this code. Ford OBDII Diagnostic Trouble Codes - P1000-P1999 - Codes Specific to Ford vehicles .: Articles

Have you checked the u-joints? Has it been driven very much at all? If not, when you drive it, it will probably throw a code if it's engine related...

If you've got a bad cop, it'll vibrate like that in OD and cause a rough idle.