This car was not manufactured in japanese. EE chassis with 2E was manufactured till 1994. With different chassis code. Like EE106 etc. And that R after EE100 is tell it's manufactured for R hand drive country.
Main differences in JDM and PKDM are as follows;1. Interior 2. Suspension.3. Engine.Remaining parts came from Japan and assembled here by Indus Motors in late 90s. Your car is PKDM. I also own the same swapped with JDM 5AFE 1.5L.