The 7.3L Power Stroke Diesel was mated up to either a ZF manual 5 / 6 speed or an automatic 4 speed electronically controlled transmission.

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Transmissions

The E4OD was introduced in 1989 with four forward speeds and reverse, utilizing electronic shift controls instead of  a hydraulic governor control mechanism.

The 4R100 replaced for the E4OD and is also a four speed transmission that is fully automatic, electronically controlled, with optional power take off. Here is a 4R100 Diagram:

ZF S5-47 is a five speed unit with five forward and one reverse speed that is synchronized in all gears with an integral clutch housing, aluminum main case, and provisions for mounting a power take-off. The identification marker is on the ID tag affixed to the transmission case. The “S” means synchronized, the “5” is the number of gears, and “47” is the maximum input torque capacity in tens of lb-ft (470lb-ft)

ZF S6-650 is a six speed unit with six forward speeds that feature a LOW gear for take off under heavy loads and an OVERDRIVE gear for highway driving and a reverse gear. The S6 also has an integrated clutch housing, an aluminum main case, extension, and intermediate housing, all of the gears are helical and synchronized, there is an internal oil pump to supply transmission fluid to an external cooler, and provisions for mounting a power take off. Here is a ZF S6-650:

Here is a copy of a Powertrain Automatic Transmission Ford Workshop Manual (Open or Save) for the 1999 F-Super Duty 250-550

Here is a copy of a Powertrain Manual Transmission and Transfer Case Ford Workshop Manual (Open or Save) for the 1999 F-Super Duty 250-550