Regarding the VIN # of the swapped motor I don't know how you would go about getting it. Here's a recent thread that has some information about how the VIN number and PCM work together. For the 2000 model year, the PCM doesn't require a VIN number anyway.
https://www.stangnet.com/mustang-forums/threads/adding-vin-to-ecu.895933/
Further I don't understand WHY it would be needed. It seems to me that the problem is bigger than just needing the VIN number.
It seems to me that the BIGGEST problem is WHY the MAF reads the same all the time. To me, it isn't a surprise the motor won't idle correctly or run right when the PCM doesn't have accurate MAF flow information.
Another option is to find a VIN number of any Mustang GT with the same model year and transmission and use that to program the VID block. The trick here is to match what the original PCM is/was expecting.
>>
P1639 - Vehicle ID Block Not Programed Or Is Corrupt
This diagnostic trouble code (DTC) indicates that the vehicle ID (VID) block is not programed or the information within is corrupt
- New PCM
- Incorrect PCM
- Incorrect VID configuration
EDIT: Here's a Ford TSB that may offer some additional information.
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Article No.
02-23-4
11/25/02
^ DIAGNOSTIC TROUBLE CODE (DTC) - P1635AND/OR P1639 PRESENT AFTER POWERTRAIN
CONTROL MODULE (PCM) OR INSTRUMENT
CLUSTER REPLACEMENT - GASOLINE ENGINE
VEHICLES ONLY
^ LAMP - 4X4 LAMP ILLUMINATED AFTERPOWERTRAIN CONTROL MODULE (PCM) OR
INSTRUMENT CLUSTER REPLACEMENT -
GASOLINE ENGINE VEHICLES ONLY
^ SPEEDOMETER - INACCURATE AND/ORINOPERATIVE AFTER POWERTRAIN CONTROL
MODULE (PCM) OR INSTRUMENT CLUSTER
REPLACEMENT - GASOLINE ENGINE VEHICLES
ONLY
FORD:
1999-2002 MUSTANG
2000-2002 FOCUS
1999-2002 EXPEDITION, F-150
2000-2002 E SERIES
2001-2002 EXPLORER SPORT TRAC, EXPLORER SPORT, RANGER
2002 EXPLORER
LINCOLN:
1999-2002 TOWN CAR, NAVIGATOR
2002 BLACKWOOD
MERCURY:
2002 MOUNTAINEER
Article 02-5-8 is being republished in its entirety to update the Service Procedure and to clarify build dates for Explorer.
This article applies to all vehicles listed with the exception of 2002 Explorer. This article applies to 2002 Explorer (SLAP) St. Louis Assembly Plant built before 3/11/2002 and 2002 Explorer (LAP) Louisville Assembly Plant built before 3/4/2002 only.
ISSUE
Some vehicles may exhibit an inoperative or inaccurate speedometer, 4x4 lamp illuminated, and/or Diagnostic Trouble Code (DTCs) P1635 or P1639 present after a Powertrain Control Module (PCM) or Instrument Cluster replacement. This may be caused by the Vehicle Identification (VID) block that must be programmed when replacing the PCM.
ACTION
As part of the calibration, there is an area referred to as the Vehicle Identification (VID) block. The VID block must be programmed when replacing the PCM. Failure to perform the proper Programmable Module Installation procedure may generate fault code: P1639 VID Block not programmed or is corrupt--P1635 Tire/Axle Out Of Acceptable Range. Refer to the following procedures to ensure the PCM is properly configured.
OTHER APPLICABLE ARTICLES: NONE
SUPERSEDES: 02-5-8
WARRANTY STATUS: INFORMATION ONLY
OASIS CODES: 204000, 204100, 206000, 690000, 698298