I think the easiest way would be to swap out the transfercase for one from a manual transfercase pickup. They probably still had an option for that in '03 on the F250 (any engine and tranny should work, as long as it's 4wd).
Otherwise, more work intensive, you can put in nearly any transfercase pulled from a fullsize Ford pickup from many years ago (possibly even as far back as the 60s) until as recent as you can find a manual transfercase. I think a good place to look is mid 90s F series. Some had a BW1356 transfercase which was available with manual shift, you would just need to make sure the Ujoints line up and the drive shafts are the correct length (although I don't think the driveshafts would give you many problems and you might just need a conversion UJoint available at most decent auto parts stores). A few other TCases that would probably work, as long as they were taken from a Ford: NP203, NP205, NP208, BW1345, BW1356, and BW4407.
