Per Marco Fernández-Sommerau's
Messerschmitt Bf-109 Recognition manual
The major difference between the E-3 and E-4 was the canopy , of course, and 50 KG of armor plate and the installation of the improved MG FF "M" cannon.
Re: Engine differences in either variant:
If an aircraft is categorized as either an E-3 / N or E-4 / N then it used the DB 601 N engine.
No mention was made of any visible differences between the DB-601 or DB-601N aircraft.
The author notes that the E-4 / B ( fighter-bomber ) may have been fitted with the DB-601 N engine.
The author also mentions that many earlier E-1 thru E-3 models were upgraded to E-4s during overhauls but would retain the original werknummer.
Hope that helps.