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My 96 GT had a motor replaced last winter. The donor was a 2000 Grand Marquis, coil on plug. We converted it to original coil packs. Runs fine in the warmer months HOWEVER, it the "Polar Vortex" is here. Runs like 3 plugwires are pulled till it gets some heat in it, then it runs GREAT.
 

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Since a 2000 Grand Marquis also has a non-PI 4.6, the long blocks are the SAME. Therefore the fact it has a different motor shouldn't really matter unless some "key" Mustang parts were not used.

Confirm that:
  • The Mustang Fuel injectors were used
  • Confirm exactly HOW the two coolant sensors were handled during the swap
  • The Mustang engine wiring harness was used.
  • Which T-stat (degree and type) has been used?

It's also possible that the poor cold weather performance has nothing to do with the swap.
 
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