The S5-47 is available for either Windsor pattern; Modular; or the diesel and 460 variations.
The ZF literature specs S5-42 as 1987-1995 Model Year.
S5-47 units as 1996-1997 MY for the Windsor pattern.
Then S5-47M only behind Modular V8/V10 from MY 1999-till Ford went to 6 speed manuals with the gas engines.
The six speed is out in terms of cost of both the transmission and the necessity to use a custom made adapter right around $800 not including the flywheel.
Yes, in the long run it will be cheaper to switch to a manual transmission. The headaches involved with keeping the Auto would surely add up.
A few quick figures with the manual transmission:
Pedal assembly from 92-96/97 truck $??
Master cylinder $60 & safety switch.
Slave Cylinder $70
Hydraulic line $40
Clutch kit $150
Flywheel resurface $35
Lengthened rear driveshaft, shortened front. $??
Transmission and rebuild components. $??
Shifter boot
Lookup some info on standalone transmission controllers for the E4OD, Bauman makes one, I'm sure you'll be way over a grand in both the controller and torque converter. Not to mention time spent wiring and tweaking the operating parameters.