The dual quads were factory installed only on Riviera and Wildcat Gran Sport models starting in 1965 model, I believe, and those were all 425's. The Rivieras were all mated with the automatic transmission. The Wildcats were available with either the automatic or a 4-speed transmission. The dual quads were not installed from the factory on the 401 in any model.
Yes, the dual quad engines had different distributors that had a different spark curve and were installed with different initial timing set. All used Carter AFBs, with the same front carbs and different rear (primary) carbs. The correct rear carbs for the manual transmission application are really rare and hard to find in the wild. Due to the fact that the number of 4-speed Wildcat GS models sold was very small compared with the automatics in the Wildcat and Riviera GS models.
The only documentation I"m aware of for dealer conversion of 65 & 66 Skylark GS's is provided in a TSB from Buick Technical Service. It's Buick Zone Service Bulletin No. 620 dated April 15, 1966. A copy is attached.
The only downside to the factory setup on the Buicks is that big air cleaner really hides all the "coolness" underneath!
Chuck