The SPI engine will drop in but a few things need to be modified. You'll need to get a modified fuel rail seeing the 99+ Mustang is returnless system and a few sensors need to be moved around and wiring needs to be rerouted and spliced. A few people here have done it, PJ, racecougar, Splitportbird to name a few. Do a search to see what's involved. Check out V6 Power also. To get it done quickly, you might be better off with the same style engine though, seeing it's the daily driver.
Well started with the basic diagonise; Coolant clean and green, Oil very dark but didn't see any sparklies when it drain out (another way to see if metal in it?), can manaul turn the crank (so its no seized right?).
Got talking to a mechanic buddy of mine, said I need to check the pan and see whats in there (to determine if rebuild is possible), he seems to think I dropped a piston and burned a bearing. If clyinder scored we replace if not proably rebuild (least the way he sounded).