Yes, Portree is Skye.
Yes, 5 1/2 hours (EDI to Skye) is easy with a pitstops, leg stretches, etc.
It tend to agree about the Killarney, Cork, Blarney, Cashel, Dublin day being long. I would add that it is not just a drive per se, but rather a day of stops at places you'll want to see. I would maybe recommend stretching that out to two days and spending more time at the stops. As an FTer you'll likely be traveling to Europe frequently, and when doing so maybe schedule a layover in DUB on the way and get your DUB fix then. Perhaps giving up a DUB day to take advantage of the time in the more far flung spots would be good?
Sorry, I clarified above, that Killarney/Cork/Blarney/Cashel would be one day. We would stay somewhere between Killarney and Dublin, perhaps Killkenny?
Is Killarney a good base or is there a better town in the area thats better to stay?