Nealboy You have not even come close to answering my question about fixing the issues presented. Terrible chat.
With an attitude like that, you will get very little help.
The simple answer is that you have lost money on this as is.
Those rafters are useless now for this application.
remove them, pile them in a save for something else pile.
Get new rafters, and proper hangers, and redo this correctly.
As per the inspectors directions.
And as Neal tried gently to tell you, built without any flashing, as it is, you are asking for rot in a year or two, do you really want to be repairing this often?
If not, listen to the voice of experience, and waterproof it.
ED