[Jeremy Weigel]

How much is your budget?
You can get a long block from Powertrain Products Inc. with a 5 year warranty for ~$3200 (+shipping?). You'll just need to swap over your intake, valve covers, sensors and accessories. As mentioned above, the engines either came from the Windsor or Romeo plant. In addition to the differences already mentioned, one has a 6 bolt crank (Romeo) and one has a 8 bolt crank(Windsor) for the flywheel/flex plate. Your VIN will tell you which you have and hopefully someone will come along with a reference to figure that out.
8 Bolt version:

1999 Ford Mustang 4.6 SOHC 2 Valve Vin X Remanufactured Engine - Powertrain Products

1999 Ford Mustang 4.6 SOHC 2 Valve Vin X Remanufactured Engine by Powertrain Products . OEM quality, backed by the industry's best warranty.

www.powertrainproducts.net

6 Bolt version

2001 Ford Mustang GT 4.6 SOHC 2 Valve VIN X Remanufactured Engine - Powertrain Products

2001 Ford Mustang GT 4.6 SOHC 2 Valve VIN X Remanufactured Engine by Powertrain Products . OEM quality, backed by the industry's best warranty.

www.powertrainproducts.net