that looks like a comprehensive and ambitous route. Some comments:
- For the museums in Dublin:
--Kildare Street is a Must
--For military history post mid 1500s and decorative arts Collins Barracks is high on the list - Red Line LUAS from Abbey Street is best means of getting there.
--If Manuscripts are your then then Trinity College is a must and Chester Beatty Library at Dublin Castle also a major location - though a lot of the stuff there is eastern.
--Make sure you take in both routes i.e.coastal and Connor pass. Connor pass is miserable in bad weather though and you wont see anything.
--Clockwise is probably best route.
-For Kinsale give Bannerman a shout. Not sure if he is still there but he was working at Charlesfort in the past and could give more detailed pointers on the area.
-For Glendalough. Its an amazing site. Even in mist and rain it is worth a visit and walk around the monastery site and as far as the upper lakes. It is also a good spot for a hike.
-For maps, as Scott has said, if you want to know every monument on the map the OS maps are the way to go - http://www.mapcentre.ie/
is a good place to get them. Its a bit off the beaten track though. I am not sure if the central tourist office just off Grafton Street sells them (cool building - converted church complete with stained glass windows)