(1) To really experience the Sahara, is Ouarzazate sufficient, or is Merzouka worth the extra 5-hour drive?
I almost got queasy at this. We LOVED Morocco, but Ouarzazate is the one place we HATED. Just awful commercialism. Remember, its the Hollywood of Morocco. Its also not really the desert, except in the same way that Palm Springs, California is the desert. Merzouga, the town, is nothing to see, but it is the gateway to the Erg Chebbi, the great sand sea that you DO want to see. This is the real desert. We took camels out to our tents and stayed in a Berber camp out in the desert. Yes, it was a tourist version of the desert life, but good enough for us!
(2) If we spend 2 days in Marrakesh, is Fes worth the 8-hour drive for another suq town experience?
I liked Marrakech better, my wife Fes. Fes is older and more traditional. Marrakech has the best of both worlds - the medieval medina and the Las Vegas-y Nouvelle Ville. I would not do the drive from one to the other just to get there, but I would do the 3-day tour we did, from Fes to Merzouga to Marrakech (you can also do it in reverse).
(3) Can anybody recommend a place off the normal tourist trail?
They are not off the tourist trail, but you didn't mention them so just make sure you look at Essaouira or Agadir (both seaside towns), and Chefchaouen (only worth the detour if you moving between Tangier, Tetouan or Fes, as its up in the north). However (again I'll tout this tour), if you take the tour we did you will see many great off-piste sites like Ifrane (the Switzerland of Morocco), Midelt (the Apple Capital), the Ziz and Dades Gorges, Ait Benhaddou, and a several other experiences like women's cooperatives where they make and sell rose and argan oil.
If I've sold you on the 3-day desert tour, just google that for several options. We recommend Morocco Fabulous Travel (https://moroccofabuloustravel.com/) but there are other companies.