My best advice is not to try to see too much in too short a time. I've been to Orkney a number of times and am contemplating a return, mainly to see some of the outer islands I haven't done yet, and when I start drawing up itineraries, it ends up being two weeks in Orkney alone, which I can't really do. So if I do go, it'll be one or two islands with an eye to returning another year for the others.
That said, you can cover all the major sights in either archipelago in three or four days. Hell, you can do it in two, if don't mind rushing all over, but you won't really soak in any of the flavor of the islands. Frankly, I think you're better off to do either Orkney or Shetland with the time you have.
Orkney is for antiquities, Shetland is for scenery. Hopefully someone else can tell you about birds, if you're interested--I'm always there too late in the season for anything much other than gannets.
I always stay in Lerwick in Shetland--it's the only town of any size, with a handful of decent restaurants and pubs. In Orkney, Kirkwall is the main town, centrally located and with better services, but I really like Stromness--it has more of the northern isles character and charm.
Mr Picky sez note that it's Orkney and Shetland, not "the Orkneys" or "the Shetlands".
And finally, Peat, have a look at the cosmetic makeover I've done on the
2007 and
2008 journals. You kicked that off (lot of damn work, thank you very much). Last year's will join them as soon as revisions are complete.
Then, It'll be the western isles, Oban area, Islay, Campbeltown and Arran and back to Dundee. I've been to Lewis, Barra, Islay and the wee toon before but however, your precious advice is very welcome! 
