Howdy All:
And Welcome Mike. The Holley Model 1940 was used as a factory replacement carb for Autolite 1100 & 1101 beginning in 1970. The '70 & '71 model year had "Autolite" embossed on it. The '72 and later had "Motorcraft". The #1940 were manufactured in various sizes and with and without the Spark Control Valve.
The Holley #1946 was the factory carb on 200s from 1980 to the end of production. They will not have a SCV.
All Holley 1900 series one barrels can be characterizes as having a rough idle and being less fuel efficient that an Autolite 1100. Their choke system works somewhat better.
The Autolite 1100 was last manufactured in 1969. It is a very simple carb and easy to rebuild and maintain. They are somewhat susceptible to dirt and contamination, primarily through the choke hot air chimney and poor fuel filtering. If I were in your shoes, I'd stick with the 1100.
Like Slade, my advice to you is to rebuild the Autolite 1100. Make sure that the carb is in good structural shape; a relatively tight throttle shaft and good mating along gasket seams. Buy a rebuild kit and start by reading the directions and studying the photos. Go slow and be careful. This is very basic stuff and would be a great father/son project. It requires nothing more than basic tools, a can of carb cleaner and the ability to read and follow directions.
Also know that many of the so-called carb problems on early Mustangs can be traced to the ignition. Before you blame the carb it might be wise to do a thorough check of the distributor/vacuum advance mechanism/ignition system to make sure that it is functioning properly. Also check for vacuum leaks anywhere.
You should also consider upgrading your ignition system with a pointless, meaning replacing the points, with a Petronix Ignitor I conversion, for a stock appearing electronic ignition system. This upgrade will make a significant improvement in idle quality and engine smoothness.
You didn't mention what tranny is in the '66, but you can make a nice improvement in performance, mileage and driveability by increasing the initial advance setting by 5 degrees over the factory specifications.
Again, welcome to the neatest forum a Ford Six lover could ever have. Check in often and read past posts and threads. There is a wealth of info here.
Adios, David