You've hit on a part of the world dear to me.
In April I bought a two-week Rover ticket from Caledonian Macbrayne and toured both Inner and Outer Hebrides.
I started at Ardrossan, to Arran, then the Kintyre peninsula, Gigha, the wonderful Islay and Jura, and back up through Glencoe to Oban.
I used Oban as a base for a few days, taking in Mull and Iona.
Then it was up to Plockton and across the bridge to Skye, staying in Portree.
Next was across to Harris, riding into Lewis, staying in Stornoway as a base.
I left for home after some minor mechanical mishaps, so missing out on Barra and Berneray and so on.
The suggestions given so far are first rate. Glen Coe is a great road, just don't get stuck on it at night. Oban seems like a vast metropolis after the solemnity of Islay.
Which way are you going to Harris? I travelled from Uig on Skye, where it is best to fill up with fuel, where there is tourist information, and where there a decent eatery. Oh, and some good Skye ales. yum.
When you are in Harris, try a loop of "The Golden Road", so called because of the vast fortune it cost to build it. To get to it, go left up the hill out of the Tarbert ferry port, and it will be signposted left further up the road. It develops into a twisting singletrack road.
There's not much in the way of amenities, just farms, grids, sheep and such, but the little lochs, heather and rocks are great for photography, and the light is excellent at dusk.
Or, instead of turning off onto the Golden Road, keep straight on from the road left out of Tarbert to reach some white sandy beaches round near the Sound of Taransay.
Back at Tarbert, take a right on the main road towards Stornoway in Lewis. Not far down the road there are views to the left where you can see sheep on the beach eating seaweed.
tarvelling up the hill, watch out for quarry traffic and rock dust, and continue climbing out of Harris until you turn back first left, then right down a mountainside, until you reach the bottom and signpost telling you you are entering Lewis.
Midway down that road you should have passed a signpost off the road on your left-hand side. This is for the Harris Walkway, where alledgedly there are good views of eagles.
Back on the road, it's a well surfaced ride most of the way to Stornoway. As soon as you enter Stornoway, there is Lewis Tyres on your left (whose services I had to use).
They don't keep motorcycle tyres in stock, but can get them within two days.
There are some B&Bs along next to the ferry port, where there is also a BP filling station, where you may meet some local riders.
Lews Castle is a bit run down, but the grounds are worth a walk.
Stornoway is a big town, so has the local hot hatch clans. The police seem to have more time though, as witnessed when they pulled over one of them for driving about with foglights on.
The Butt of Lewis is worth a visit if you are a keen birdwatcher. The Gneiss rocks are covered in gulls and shag, and there are oystercatchers on the nearby beaches.
Dun Carloway, as also mentioned, is good for photography, with views over the smaller islands.
Make sure to visit Arnol, where you can see the Black house and White house, examples of Lewis homes.
The White house is the newer one, and the black house was occupied until about the 1920s.
At it's heart is an open peat fire, and has a built-in byre.
Calanais standing stones are older than Stonehenge, and shaped like a Celtic Cross. Definately visit here, and the smaller stone arrangements within walking distance.
I never had any plans in concrete, instead working things around the ferry timetables.
There are some photographs here...