The autolite C6af L originally came on a 352. The 4100 is a great carb. The only problem with them is they are 50+ years old, and have been rebuilt untold number of times, and parts have been changed and there is no master set of serial numbers--that I know of--a person can check to see if you have the correct parts. I assume those books/guides died with Jon from Pony Carbs.
It should have .048 jets. Mine ran best with .046 jets primary. I'll be very surprised if you can even get the secondaries to open. I'd run .050--.052's in the secondaries if you can even get them to open. I say that b/c they are operated by vacuum which flows through the air horn, and it is a persnickety system. Yes, persnickety!
If you have one of those heating plates between the carb and manifold use it. Check Allcarb for jets. Mike's carbs sells them too, but his are hand drilled with a machine burr around the orifice.
**Note: If you can hold the throttle shaft and move it slightly up and down with the carb absolutely stationary, then it needs to have bushings installed and if you don't have it done it will drive you batty trying to get it to run right.
**Note #2: The smaller 1.08 venturi 4100 is 480 cfm, not 400 cfm, as you mentioned. Also, just because you want need a 1.08, be aware there are two vastly dissimilar designs of the 1.08: small block and big block designs. You want the small block design that came on a 289. Run the numbers on website mustang tek to check and know.
**Note #3: The kits usually don't come with the accelerator pump diaphram. It costs extra.