Wrong!!!!!!!!!
The 427, 428, Boss 429's had large diameter input shafts (and 31 spline output shafts), but the 390 has a smaller, more normal diameter small input shaft, but it is shorter than a SBF. The actual area that is shorter is the part that goes into the input shaft. I have had several 390 and 302 (plus a 429CJ) Toploader transmissions over my 33 years of running Mustangs and know the difference when I see it.
Anywhays, see
http://www.5speeds.com/toploader.html and
http://www.carmemories.com/cgi-bin/viewexperience.cgi?experience_id=184 and several other sites for the info on shaft diameter.
The C60R-7A040-C tailshaft is correct for a Mustang so you are good to go there (again found on the site I referenced earlier.)
The only remaining issue would be the input shaft. The small block shaft for a SBF has a 1 1/8" length pilot bearing shaft length (shank) and the big block (all) have a 3/4" pilot input shaft length (again from David Kee Toploaders.) You can use a cutoff tool and grinder to make a sbf input fit a big block, but science hasn't perfected a way to make the big block Ford input shaft any longer.
It is possible to acquire one from a SBF to replace the 390 one because they are other wise the same, but unforunately it requires that a fair amount of the tranny be disassembled. Another, less desireable way is to purchase a "step" pilot bushing from a mid-70's pickup. It is longer than a normal pilot bearing and is able to capture the shorter input shaft. I don't recommend this approach though.