I'm probably much more of an urbanite but I'd definitely devote some time to Glasgow and Edinburgh. Edinburgh is arguably the most attractive city in the UK and Glasgow is renowned for its cultural scene.
I don't know exactly what your interests are but if you visit Glasgow I would recommend:
Drygate and/or Brewdog - if you want to try beers from local craft breweries.
Nice 'n' Sleazys, Mono, Stereo, the 13th Note and the Art School - if you would like to explore the music scene.
Guitar Guitar - has a pretty good range of pedals.
The Kelvingrove Museum and Art Gallery - one of the best museums in the UK outside of London.
A good railway journey from Glasgow might be:
Glasgow Queen Street - Balloch. This would give you access to Loch Lomond and the surrounding area.
Balloch - Dumbarton Central followed by Dumbarton Central - Corrour. One of the most remote stations in the UK but there is a hostel relatively close.
Corrour - Fort William. It's probably worth climbing Ben Nevis if you're that way inclined.
Fort William - Mallaig. I would then get a ferry to the Isle of Skye.
From Skye you can get a bus to Kyle of Lochalsh train station where you can travel on to Inverness and back down towards Edinburgh if required. You can also travel north from Inverness or across to Aberdeen.
http://www.seat61.com/WestHighlandLine.htm#.VSKmOMZH2Rshttp://www.theskinny.co.uk/events