My wife and I got married in Scotland six years ago, then toured the country for our honeymoon. We went back a couple of years ago for a get together at her clan's ancestoral home, Selkirk.
First off, forget the train, they don't run anywhere you really want to go. It's not like the rest of europe where you can take a train anywhere. Get a rental car and start driving, it's not a big deal to drive on the wrong side of the road, you'll pick it up pretty quick. The roads are good and not very crowded, I was suprised at how rural most of Scotland is, it doesn't have nearly the population density as England hence the lack of trains. You can get to Edinburgh by train but beyond that forget it. Edinburgh's great but the real beauty of scotland can only be found by car.
There are castles everywhere so get a guide book and take your pick. The Borders region is cool, stop in Selkirk for some tweed and see Sir Walter Scott's house Abbotsford. Definitely see Edinburgh and the castle there, and walk the royal mile, take in Rosslyn chapel. Hit Stirling and it's castle as you go north, and go to St. Andrews just to say you've walked on the Old Course. St. Andrews is a neat college town also so it's a nice place to spend a day. If you can find some going on hit some real highland games, we found one in the town of Ceres that had been going on annually for almost 700 years, it was originally chartered by Robert the Bruce. Hit Balmoral (the queen's highland manor), and Glamis castle where the queen mother was born. They have a thing called the whisky trail where you drive the route between a bunch of distilleries. We only hit one but it's a treat. Of course see Loch Ness and Urquhart castle, and Culloden battlefield. Read up on the Jacobite rebellion before you go so it'll make sense. Cawdor castle (Macbeth) is nearby also and interesting. The town of Inverness doesn't have much going on, but is a good place to overnite.
The west coast is very pretty, but we didn't make it to the Isle of Skye or the other Hebrides but people say it's the prettiest part of Scotland. It's on our list for next time.
Rent a car, get a decent guide book and start driving. Hit the big attractions then just wander after that, you'll find neat stuff at every turn. Eat in pubs but don't expect wonderful food, it's basic comfort food but not a lot of michelin rated stuff. The best advice I can give is to stay in some Bed & Breakfasts, there are a bunch of wonderful ones throughout the country and the owners really take pride in them. You'll only pay about half the price of a hotel and get to meet people you wouldn't normally get to meet, plus most of the B&B's are really nice. The Scots are famous for their hospitality.
You'll have a great time I'm sure.
