If you have an extra 4" long bolt its one of the manifold bolts. Check to make sure all your manifold bolts are there. Look up the manifold bolt pattern on google for a diagram, IIRC the longest ones go on either side of the tstat housing.
And yes you have a fuel leak somewhere, most likely an injector is not seated right. Remove the rail, check all the O rings, re-seat them and make sure the rail is seated down on all the injectors. There will be no dampness or fuel smell if it is done right.
Why did you do a 2-3 hour job over the course of many days?
2000 Mustang GT Steeda #0048
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.