When I did mine I also went Coil on plug with an LS based tune and some wiring mods, but I have also done a couple 350's. There isn't any difference as far as the PCM swap goes though between the two motors.
If you can find a 98-01 top kick or Kodiak, they have the L21 7.4 with coil near plug and 0411 from factory. Or at least look at the schematics from those for reference.
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