The only difference between the E-1 and E-3 was the guns iirc. The former had 4x 7,92mm, the latter 2x7,92 + 2x20mm MG FF.
I am not sure about the armor, so far no literature on it was clear and free of controversies; I believe both the E-1 and E-3 had the pilot armor from the start, the up armoring was in fact adding the pilot`s head armor after the Battle of France to all models.
Neither there was any difference between the engine models. All Emils, except the /N versions which mounted the DB 601N (from June/July 40) , had either the DB 601A-1, the A-1 with improved supercharger or the slightly more powerful DB 601Aa with higher boost (1.35ata for 5mins and 1.45ata for 1min vs. previous 1.3/1.4ata).
The front armor glass was also available for certain, but you don`t see it often until the F-4; I guess it had more to do with the lack of enemy daylight bomber presence rather than supply issues.