For rugged scenery I'd recommend starting your trip from way up north (Inverness maybe) and then cycle up to Cape Wrath in the far north west corner of Scotland. From there you could meander down the coast and spend a few days on the Isle of Skye (there's a bridge to the island) and then meander down yet further south and catch the ferry onto the Isle of Mull. Its possible to cycle around Mull and then get a ferry from the other side onto the Kintyre peninsula. You can then cycle round the peninsula and get another ferry onto the Isle of Arran, then cycle round Arran and get another ferry back onto the mainland and end up not far south from Glasgow. From the ferry port (town called Adrossan) you could cycle across country through Dumfries and Galloway and the Borders region - not quite as rugged as the highlands, but still very hilly and very few tourists bother going there. The minor roads are usually deserted.
Some spectacular scenery here and many parts feels very remote depsite the fact that you're never actually that far from a town or village. I wouldn't recommend Loch Ness - its very, very ordinary compared to the rest of the highlands, only its somehow acquired this mythical status. Overrun by tourists all summer as well.
If you haven't found it already, I'd recommend you look at -
http://www.sustrans.org.uk - they build and maintain cycle routes throughout the UK (some on minor roads, others purpose built tracks) and also make cycling-specific maps.
As for the time of year, June - August is peak season for the midges. They'll only be a problem if you intend to camp. If you plan to wild camp (possible pretty much anywhere in Scotland) then carefully selecting an exposed, windy campsite helps a bit.