I think the best thing would be to open the engine and inspect the damage.
Could be as simple as new bearings or the block could be damaged...pistons, crankshaft, rings, rods, etc..
Depending on that you have several options, but the one that would give you less trouble is buying a new or rebuilt short block (worst case scenario).
When you look for a donor 4.6, select one from a 2000 or newer model. Plenty of sources available: crown vics, F trucks, Mustangs, Explorers.
Rob Hernandez, AFM co-Founder.