I can tell you this;
A few years back I tried using a CDI box off a 2nd gen 300 (I think it was around a 94), on a 1st gen (If I recall correctly it was a 89) what I found was, when I went to install the CDI box, the plugs on the CDI were opposite of the plugs on the harness, (big deal right?) so I just went ahead and re-arranged the harness plugs and installed CDI ------- NO SPARK (I thought this was odd because I know its a good CDI.)
To verify CDI is still good I Go back to original harness, test it ------- good spark.
I can tell you for some reason there IS a variation throughout the years (I cannot remember which years) but they wont all interchange.
A quick way to tell is by verifying the plug orientation on the cdi itself. some of them will have the alarm box plug to the left, some have the alarm plug to the right.
keep that orientation with the harness and your good to go.
I'm sure that sounds confusing, but its how it has to be if your swapping CDI's.