The difference is in the bellhousing pattern as 02X said. There is no electrical differences between 99 and 2000. That bump in the bottom of the pan is for a 4x4 filter. The flatter pan is for a 2wd. You should be able to buy the correct filter for your application and use the matching pan.
The bellhousing is removable, but it comes off as a unit with the pump. This is where you could run into a little changeover issue. They used different pump sealing ring and thrust setups in those years. They have to match the coast clutch drum.
If you have a decent trans shop in your area, and are clear with them what you want done, and that you don`t expect any warranty, they may be very reasonable about swapping the necessary stuff for you.
The other thing you may have to watch for, is the sensor setup along the top of the case, Ford was all over the place in those years. Some had an output sensor on top back by the tail housing, and an input sensor up by the bellhousing.
The only way you`ll get in trouble there is if your vehicle needs one of the sensors that the case your putting in doesn`t have. If your swap case has a sensor in it that the vehicle doesn`t use, then no big deal.
Last, I would also stay with the converter from the vehicle unless it is bad. At least measure the pilot. There are two different pilot lengths. If your converters match, then you can use either one. The stall is the same.
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