As far as I know, there have been no changes in Electoral Division boundaries except in urban areas, where urban boundaries have been extended or Electoral Divisions rejigged as in Dublin. shanew's "Toponymy resources" seems the simplest to use for rural areas.
hi - I believe I can do a match up on the 1851 townland database between civil parishes and 1901 DEDs, if that helps. A spot check of the query output is looking quite good. It's based on a match by townland name, civil parish, barony and county - so can fail with compound barony names e.g. Kilkea and Moone vs Kilkea & Moone etc., but might provide a good starting point for rural areas.
Extract of the query results (151 in total) returning just the parish, barony, DED and county code fields for Donegal below - if it works out then the next step would probably be to import the shapefile coordinates and match up to the civil parish names.