Egyptian Arabic does differ a little from standard Arabic in that j is pronounced as g. But this is a case of Egyptians changing the pronunciation of Arabic to fit their own linguistic habits. For example, the name Jamal is pronounced Gamal in Egypt. We don't know how vowels were pronounced in Ancient Egyptian. Different dialects of Arabic pronounce the vowels all differently anyway.
Vowels are much more variable than consonants.
It would be logical to think that the Greeks in Alexandria might have influenced the native language of Egypt, however Coptic has many special letters to indicate Egyptian sounds that did not exist in Greek. Ancient Egyptian kh became sh in Coptic, but this isn't because of Greek influence because Greek didn't have any sh sound. I just picked up Cerny's Coptic Etymological Dictionary to pages 220-1. There are about 17 words. Only one is borrowed from Greek on these two pages.