Gotta agree with Ascot (*almost faints*) with the suggested trip around Scotland. Not only does it cover massive amounts of track through the night (I don't know how much of it you need) but the Kyle line is absolutely amazing (I've got photos somewhere on here, I'll upload them, of the scenery on the line). Also agree that it was well nice to sit in FC on that line as it's Standard only. Not much difference in the seats IIRC, but it's one of those few lines you can do such a thing on. I've not done the ferry and bus bits as we went up there for the SRPS tour with the 47s at the time, but it does sound like a good way to include things like the Isle of Skye (would be criminal to go all the way up to Kyle and not visit the Isle!) and getting The Jacobite in. Don't forget that's additional charge as the ALR is not valid on it.
My main recommendation however is to ensure you charge your batteries for your camera (assuming you use rechargeables) before getting to Scotland. Why? There's so much fantastic scenery up there you'll want to take lots and lots of photos.
And unless you're a very light sleeper/very excited about the upcoming trip (like me) when on the sleeper, you might not enjoy a sharp stop in the platforms at Edinburgh Waverley for the change of coaches at 0345 (or thereabouts), the stop was such that I nearly got sent flying down the train when we got to Edinburgh last time! Hopefully it's usually more reasonable than that! You'd get around an hour of GM noise irritating you under the roof at Waverley before the Fort William portion departs at 0450. When it was 37s, the ticking-over of that EE engine was divine under the roof. I get to compare EE with GM in the same conditions in about 6 weeks, I'll let you know if I get driven mad by it
So going south is actually more reasonable (arrive around midnight as Ascot says, leave within 30 - 60 minutes) and you're more likely to be awake. Of course, if you do the berths on the Fort William line you'll not need to change anyway.
As for the FGW sleeper, as 91101 says, it is declassfied throughout in the seated sleeper, using ex-First Class seats. Beware the head cushions though, they are not very soft! But the seats do recline a bit to make sleep slightly easier (I tend to sleep leaning on the table, head on top of folded arms with a coat between the head and arms, when on the train so it doesn't help me). Never done the berths with FGW, always fancied it.
Berths are usually available until departure time with FGW, although at weekends, especially in summer time, they might sell out. Be prepared to ride the cushions if so. Mid-week you should be OK. And who knows, you might be lucky enough to get a Duff hired-in on the day you do it?
I hope there's something useful to you in the above post.
Julian