There's no particular reason for using a Saginaw, other than availability, (newer) and possibly a slightly more efficient 2-3 synchronizer on the Saginaw. If you've got a Muncie handy, I'm pretty sure it would work. I'd suggest making up a slip yoke for the "output" by using a couple of clutch disc hubs, machined down to fit inside a slip yoke with the splines bored out, then welded into place. By drilling a series of holes in the slip yoke, and "plug welding" the clutch splines in, you'll have a sliding fit, without destroying the input shaft on the 3-speed. The carrier bearing could act as your rear shaft support, so just rig a rear crossmember to support the bellhousing bolt pattern, and make another crossmember under the rear mount position on the 3-speed. For shifting, I'd use one of the vacuum-shift setups for 4 wheel drive transfer cases, with an electric solenoid or a manual vaccum valve for shifting. Spring-load the shifter in one direction, and use the vacuum chamber to shift it the other way.
Jerry


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