In retrospective, it was safer this way as it was neither safe to run on the road nor with a better understanding of the trail system. Besides, the road to Fort Augustus after Foyers gets pretty far from the Loch and hilly, so you'd better find and stay on the official South Loch Ness trail. By the way, the full loop is 81-mile long, that would make for quite an ultra!
Bottom line, sorry my post isn't much helpful in case you are planning to run while in the area and... looking for Nessie. Hope you are more successful and, for those interested in a bit of virtual tour of that section of the Loch Ness, here are a few pictures below.
First view of the Loch Ness coming from Inverness.