You might want to check out the Great Glen Canoe Trail http://greatglencanoetrail.info/. When I was walking the Great Glen Way in 2011, I found out about the Canoe Trail and thought it would be fun to do in a packraft. Caution would be needed on the bigger Lochs as they can get quite choppy, but the benefit of the packraft means that you can bail to the Great Glen Way if you had to. Doing it West to East means that the prevailing winds are usually at your back.
The lower section of River Spey a great paddling trip - http://www.canoescotland.org/AccessEnvironment/RiverSpeyGuide/RouteDescription.aspx. In Oct 2012, I did a trip from the Head Waters at Loch Spey to the A96 Bridge. I mountain biked into Loch Spey but it could be done in a day of walking. The water levels were very low that year so I had to walk my raft a lot the first two days (cold feet in Oct). The lower section of the River Spey (often referred to as a River Spey decent) is a popular multi day trip for paddlers and I wish that I had focused on that part of the river instead.
Lots of other options in Scotland that will come up if you Google Packraft and Scotland, but I did not have my raft long enough while in the UK to plan more than one trip.