Well it might not be the correct Stonewells, but Moray and Banffshire had pretty fluid boundaries for a while (from my understanding) so it's possible that the town/parish straddled the boundaries or changed county altogether at some stage.
There were some fluid borders between Moray and Banffshire, but not west of the Spey, which is where Urquhart is. There was also some adjustment of boundaries between Urquhart and Speymouth. However there is no possibility that a Stonewells in the parish of Gamrie in the county of Banff could have 'migrated' from the parish of Urquhart.
In fact Stonewells is still there, in Urquhart. It is marked on the Ordnance Survey Landranger and Explorer maps, and a search for Stonewells on
www.streetmap.co.uk produces a reference to both this one and the one in Gamrie, Banffshire.
Did you search the Gazetteer on GENUKI? You need to be aware that this is very incomplete, and that Banffshire is much better covered than Moray.
For a photograph of Stonewells in the parish of Urquhart, see
http://www.geograph.org.uk/photo/201868 The other places mentioned are as already suggested. Dipple is on the left bank of the Spey a few miles south of Urquhart; Folds of Innes would be somewhere around the Innes estate and Cowfords is just south of the main A96 road and just west of Mosstodloch.