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The A does not stand for anything, it is just a family.
The 3406A was a fully mechanical engine that was produced through the mid-1980s The 3406B was a mostly mechanical engine (some electronic components? which?) that was common through the early to mid 1990s 3406C was a hybrid mechanical/electronic engine (what parts were mechanical? what parts were electronic?) The 3406E was the fully-electronic version and sold on trucks until EPA requirements became too tough