'99 Taurus engine into a '98 Taurus

If the calibration of the engines are not the same, you're looking for problems, the pcm in the receiving car may not be able to accurately monitor and control the engine performance, not saying it wouldn't half-assed run, however there may be issues which would prevent it from passing, if you need to, emission testing, sounds risky to me.

PCM is powertrain control module, the brains of your vehicle, what I'm saying about calibrations are this: the engines must have the identical components installed on each in order for that particular pcm is properly run the vehicle, just because each is a 3.0 or whatever really has no bearing on anything, the days of swapping out engines, firing it up and driving away into the sunset, are no longer as easy as it used to be, yeah you can put another engine of the same size in there, it'll most likely run. Run optimum, that's another story. Research the info you need, calibration sticker should be on the engines somewhere, get the codes and consult the dealer to see if you can do it properly, why would you want a car that runs, but doesn't run optimally?

Same engine, possible different emission calibration, it's not the mechanicals of the engine to be concerned about, it's the specs for the emission controls, etc. I would check with the local Ford dealer, get his take on engine swaps. From the service manual:

Each vehicle has a decal (Figures 1, 2 and 3) containing emission control information that applies specifically to the vehicle and engine. The specifications on the decal are critical to servicing emissions systems.
In addition to the tune-up specifications and procedures, the emission decal shows a color-coded (shown in black and white) schematic of the engine vacuum system. The color coding on the schematic represents the actual color coding on the vacuum hoses. However, there will be instances when a hose color does not match the color on the decal.

Decal Location

Typical location of the decal will be on the underside of the hood or the radiator support sight shield.
Powertrain Base Calibration Information

Powertrain Base Calibration Information is located in the lower right corner of the Vehicle Certification Label. Only the Base Calibration will appear on this label (Figure 3). The Revision Level is no longer printed on the label, however it can be found in On-Line Automotive Service Information System (Oasis). For the 1999 model year Ford Motor Company is using two different Protocols which describe Powertrain Base Calibration. The Protocols are designed to provide worldwide standardization for vehicle calibration. If electronic engine control strategy is carried over to the 1999 model year from 1998, Protocol 1 is used (see Table 1 below). New strategies for the 1999 model year use Protocol 2 (see Table 2 below). For more information on Vehicle Certification Label, refer to the Workshop Manual.

Figure 3: Typical Vehicle Certification Label with Powertrain Calibration Information

Decal Location

Typical location of Vehicle Certification label is on LH door or door post pillar.

I would guess that it's certainly probable that the car would run, not saying it would run like crap, only the chance that it's going to possibly create some headaches where in the end you would have wished you hads purchased a complete ready-to-run vehicle. If you don't have the need to pass emission testing for vehicle inspection or whatever, that's a plus in your favor.

Np prob, I understand your situation, just trying to give you some info.