I don't know if it is a running problem with the kit. but when I built it I discovered that the engine covers would not fit properly by a good 1/16th of an inch in some places. So as a result some top parts of the engine had to be removed and the inside of the covers shaved in order to get the covers to fit. I couldn't see any plastic warping and the engine did fit into its proper position in the fuselage. So as a result I had no option but to glue the covers into place.
The E-3 was replaced by the E-4 (with many airframes being upgraded to E-4 standards starting at the beginning of the Battle of Britain) which was different in some small details, most notably by using the modified 20 mm MG-FF/M wing cannon and having improved head armour for the pilot. With the MG FF/M it was possible to fire a new and improved type of explosive shell, called Minengeschoß (or 'mine-shell') which was made using drawn steel (the same way brass cartridges are made) instead of being cast as was the usual practice. This resulted in a shell with a thin but strong wall, which had a larger cavity in which to pack a much larger explosive charge than was otherwise possible. The new shell required modifications to the MG FF's mechanism due to the different recoil characteristics, hence the MG FF/M designation.
The cockpit canopy was also revised to an easier-to-produce, "squared-off" design, which also helped improve the pilot's field of view. This canopy, which was also retrofitted to many E-1s and E-3s, was largely unchanged until the introduction of a welded, heavy-framed canopy on the G series in the autumn of 1942. The E-4 would be the basis for all further Bf 109E developments. Some E-4 and later models received a further improved 1,175 PS (1,159 hp, 864 kW) DB601N high-altitude engine; known as the E-4/N; owing to priority being given to equipping Bf 110s with this engine, one fighter gruppe was converted to this version, starting in July 1940. The E-4 was also available as a fighter-bomber with equipment very similar to the previous E-1/B. It was known as E-4/B (DB 601Aa engine) and E-4/BN (DB 601N engine). A total of 561 of all E-4 versions were built, including 496 E-4s built as such: 250 E-4, 211 E-4/B, 15 E-4/N and 20 E-4/BN.