Definitely get the 4.10. I have had both and the 4.10 are way better than the 3.73. Also, you are going to need a new computer chip to make the 4.10 AOD-E friendly. Several places burn them, I know Dallas Mustang does as well as others.
As for shift kit, you may want to also consider the Transgo or the Baumann. They are the superior product compared to the B&M.
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1991 Mustang GT - Cobra Intake, FMS 65mm TB, C&L 73mm MAF, GT-40P heads, Crane 2031 cam, Crane 1.7rr, Built AOD, Art Carr 2400 non-lockup converter, Transgo shift kit, BBK chrome cold air, FMS 'P' headers, Pacesetter off-road H, BBK aluminum pulleys, 2-C Flows w/ dumps, 4.10's, Steeda STB, for now...
The Original GT-40P Tech Page