So....it's now running in HO firing order....correct. This should alleviate your feelings a little. At the very least, you know now that it's a roller block (or roller block conversion) with an HO camshaft. And from what you know, you’ve already got hypereutectic pistons in there, which isn’t such a bad thing and the stock HO intake. Now all you have to wonder about is the heads and you’re all set. If memory serves, when you pull a valve cover off, the E7TE heads have the letter “T” stamped on them near one of the pedestals of the valve train. This signifies “Truck” which is what these heads were pirated from, before they made their way to the Mustang.
On last thing....make sure to separate the number 7 and 8 sparkplug wire from one and other (just swap them to opposite sides of the spark plug wire looms). Having them directly beside one and other sometimes causes misfires that could lead to big problems at high RPM.