Differences can include most anything- some of the more common are the PCM calibration, exhaust, gear ratio, RPM range and limits, hardware, mounts (just to name a few). With the wide number of models released, differences will vary from one comparison to another, and there may be other differences not noted.
No definitive and exhaustive "list" has been released to my knowledge.
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Still consider myself a "Marine Apprentice" after 47 years (learn something new every day).
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Mercury 250 proxs 2B115089