You'll have to make a number of strategic choices one being do you go for
1) the "big name" sites on the islands (Orkney, Lewis) accepting that narrow roads and ferry timetables will considerably limit how much you can get round - but you will come back having seen the best of Scotland, or
2) stay on the mainland (probably south of the Great Glen where the roads are best) and get round many and a more varied selection of sites.

Here are some thoughts on option 2 assuming you have 14 days. Where I've mentioned sites by name, they are usually Historic Scotland or Local Authority run so you'll get info boards, parking and easy access. They'll be a bit manicured, of course. Worse still, there may be other people there. But if you don't know Scotland, it might be a good place to start. They won't fill out the day so you'll need to add some others from what's on TMA.

Obviously, you could do this in reverse depending on your most obvious entry point to Scotland - Berwick or Carlisle.

DAY 1
Get to Scotland. East coast Borders. Edinshall broch (not a typcal one).
DAY 2
Around Edinburgh. National Museum. Cairnpapple henge (check opening times). Glenrothes henge, mortuary enclosure (?), stone circle with rock art.
DAY 3
Angus souterrains and Pictish stones/Museums.
DAYS 4/5/6
Aberdeenshire stone circles and Pictish stones.
DAY 7
Clava Cairns and Corrimony.
DAYS 8/9/10
Kilmartin Valley. A bit of a drive from Corrimony but not really worth bothering with anything in between when you'll see better at Kilmartin. Rock art, stone circle and alignments, henge, chambered cairns. Great wee museum. A mainland must see.
DAYS 11/12/13
Another longish drive but worth getting down to Dumfries and Galloway. Cairnholy chambered cairns, Torhouskie stone circle, rock art. Ballochmyle worth stopping at on the way.

Hope that helps.