Engine swap

They are both a vin V so they should be the same engine and the engine is removed from under vehicle, with transmission attached.
ENGINE > REMOVAL
Disconnect negative battery cable. Disconnect steering column at pinch bolt joint in passenger compartment. Remove engine appearance cover. Disconnect wiring from intake air temperature sensor. Remove air cleaner outlet tube.
Release fuel pressure, and disconnect fuel lines. See FUEL PRESSURE RELEASE & FUEL LINE CONNECTIONS. Discharge A/C system using approved refrigerant recovery/recycling equipment. Drain cooling system. Disconnect main vacuum hose from intake manifold. Remove ground straps from bulkhead.
Disconnect wiring from powertrain control module, mass airflow sensor, and evaporative canister purge valve. Disconnect 2 connectors mounted on brake booster. Disconnect accelerator and cruise control actuator cables from throttle body. Remove oil dipstick and dipstick tube.
Disconnect cable from lever on transaxle. Disconnect wiring from secondary air injection pump relay (on top of transaxle). Disconnect necessary vacuum and coolant hoses. Disconnect transmission fluid cooler tubes from transaxle. Disconnect power steering return hose from fluid reservoir. Disconnect wiring from alternator.
Raise and support vehicle. Remove front wheels. Disconnect left and right ride height sensor links from lower suspension arms. Remove front stabilizer bar links. Separate left and right lower control arms from steering knuckles at ball joint. Separate left and right tie rods from steering knuckles.
Remove left and right axle halfshaft nuts. Pull left and right axle halfshafts from hubs. Drain engine oil. Disconnect and remove exhaust "Y" pipe. Disconnect power steering pressure hose from oil cooler connection.
Remove lower radiator hose. Remove starter. Using Disconnect Tool (T81P-19623-G2), disconnect refrigerant lines from A/C compressor. Using Powertrain Lift (014-00765) and Bracket (014-00766), support front subframe/powertrain assembly.
Remove 8 front subframe retaining bolts. Lower subframe/powertrain from vehicle. Disconnect power steering pressure hose from power steering pump. Using engine hoist, lift powertrain from powertrain lift and place on work surface.

The 1998 Lincoln Continental V8-4.6L DOHC VIN V ECM part numbers are for Federal emissions, F7OZ12A650EG and for California & Mass is F7OZ12A650FG.
The 2000 Lincoln Continental V8-4.6L DOHC VIN V ECM part numbers is YF3Z12A650AA.
The main part of that number is the Z12A650, so I would have to think that it would work, but seriously, I have searched for over 1/2 hour and still cannot find a definite answer mostly because I can not even find anyone who sells either ECM.
If the connections fit, I would assume it may work. It may need to be programmed to that specific engine and vehicle.