Hi Matt, like Chris I spend my hiking time in the Scottish Highlands and am slowly gaining experience backpacking and wildcamping. To answer a few of your questions:
2) Footwear/Gaiters - I don't like gaiters very much and generally don't use them if I know there is a good path all the way (common on the more popular mountains). However, going off piste can mean heather and bog, and gaiters are really helpful here. Another thing to watch out for is the tick which are getting quite bad on the west coast. Gaiters can help protect you against these as their favourite haunts are tall undergrowth like ferns and bracken. For footwear, if you don't go with waterproof socks then make sure your trail shoes are quick-drying!
3) Water - like Chris I have never treated water in the Highlands. Obviously you drink from streams at your own risk but I think as long as you are sensible about taking it from high up, checking upstream first, and only taking from fast flowing water, then you shouldn't have a problem.
4) Maps - an alternative to the new OS Get A Map service is to register (free) with the Walk Highlands website (http://www.walkhighlands.co.uk) which offers access to OS Maps (both 1:50,000 and 1:25,000). You might have to play around a little to get maps printed but you can definitely plot and view your own routes, as well as using the routes already available on the website. Another alternative is a subscription service through a website called Grough (http://www.grough.co.uk) or you might look at proprietary mapping apps/software such as Memory Map or Viewranger.
I hope that is of some help to you. Good luck with your trip. I'm sure the Cape Wrath trail will be an amazing experience