Hi Waken !!!
According to AJ-Press publication "Monografie lotnicze" no.42, the E-1 and E-3 versions were produced simultaneously in proportion 47% E-1 and 53% E-3.
By the time when the production of Emil was finished in summer 1940, 1082 Bf 109 E-1s were assambled and 1171 ( the other source-1174) Bf 109 E-3s were mounted.I've found also info that some of the first E-3s were equipped with four MG17 machine guns.I hope the answer was satisfying for You.
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