Hi
is the A939 then A 86 the best route to take to get from Nairn to fort William with a little side trip to Dufftown to try the speyside distilleries?

Welcome to Fodors. That's probably not the route I'd take. I'd take the A96 to Elgin, then the A941 to Dufftown, then back north to the A95 and A95/A9/A86 to Ft William.

That does involve a little detour down to Dufftown and back but is more direct than the A839.

BUT . . . what is the rest of your itinerary like? There may be distilleries more convenient elsewhere in your trip (even though all the whiskies taste different -- every distillery and it's tour is pretty much like every other distillery). And of course one of you will have to skip the tastings to be the driver.

You have to skip the tastings there and then as the driver but most offer samples to take with you for the driver.
Last tour we did we were sleeping in the distillery car park (in a campervan) so that was ideal, though I am not a whisky drinker so I took mine out to the van for DH to have later in the evening.
One tour is much like another, apart from the tastings, which some charge extra for whilst others include it in the price.