The Cicerone End to End to Trail describes an off road route from the end of the Choire Lodge access track to John O Groats if you go that way. If you're lucky you may get a preview of p390-99 at Google Books. I've heard from someone thats tried it thats its anything but easy going though (bogs, blocked forest paths, downed bridges etc).
Also of interest may be the Ca na Catanach, the old drove road between Kinbrace and Dorrerry, from where you can cut across to the north coast and follow this to John o Goats. Again this is described as challenging with rivers, deer fences and bogs to cross.
I haven't tried either of these myself, I just gritted my teeth and kept to the roads.
Too late for you now, but just for reference, there's an easy route from the PW to the WHW mostly on waymarked trails, St Cuthberts Way to Melrose, Southern Uplands Way to Traquir, short way on road or over the hills to Peebles, John Buchan Way to Broughton, a signposted RoW and tracks to Lamington, over Tinto to the Falls of Clyde, then the Clyde Walkway (finally complete)and Kelvin Walkway to Milngavie. The centre of Glasgow may be avoided by cutting across to a level crossing just north of Coatbridge (NS722673) from which an old railway may be easily followed to (annoyingly) a mile before the WHW joins the railway south of Drymen. Theres's a parallel track for this short stretch though.
Edited: 08/02/2012 at 15:49