Your best option would be to run a 96-97 ex ECU and harness. Remember, your mark 7 uses a return style fuel system, the 99-01 uses returnless and also is slightly different in the wiring department. Also, the 96-97 systems use the standard VSS in the trans/tcase location, not the VSS located in the rear axle. To use the 99+ system is not impossible by any means, but it does require changing the fuel pump sending unit in the fuel tank as fuel pressure is regulated in the tank (as of 99), and not on the fuel rail (like 96-98 ex's) I understand you may have the 99-01 parts, but it would be best to change/swap for the earlier system, it will make it much easier on you...
Why do you want to switch the lincoln to OBD2??
SVT
My spare Explorer parts include a 1998 dash harness, PCM, battery/alt harness, and under hood harness, GEM module.
I was planning to use the 98 PCM, but I know it has PATS, and the 96/97 may have a little less wiring(PATS module).
Will the 1996/97 Explorer PCM accept just the VSS signal directly from the trans tail shaft? That would solve that question of the ABS VSS signal etc.
I'm changing from EECIV because I've never liked the idea of spending tons of money on aftermarket devices to "trick" the computer into working with modifications. Now there are new aftermarket devices that can do very well, but those are completely unlike the SCT flashers for OBDII+ systems.
I'd prefer to learn one less method for tuning, the OBDII to current way, and skip the EECIV stuff. Way back when EECIV was considered low tech compared to OBDII. Now people are doing very well tuning the old EECIV cars, but I'd rather skip that.
I have one last reason to upgrade my 91 wiring. Ford was redesigning their wiring systems in the 90's. That's when new relays came out which swap between each other, all throughout the vehicle. I hated the old relays and wiring connectors. The Explorer was also part of the beginning of low current wiring inside the car, keeping as much of the high powered circuits under the hood etc. They also had master electrical control to monitor power loss, and cut power when headlights etc, are left on.
I'm going to try hard to install a GEM module, which gains me the better electrical control, plus a cruise control which I lose with a PCM change.
The V6 Explorer/Ranger swap are relatively simple because the 302 came in the perfect cousin vehicle. The Explorer parts are direct swaps.