The trans and transfer case must be drained separately they are not interconnected for the fluids
SECTION 307-01C: Automatic Transmission — 4R100 1998 Expedition/Navigator Workshop Manual
IN-VEHICLE REPAIR
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Transmission Fluid Drain and Refill
Special Tool(s) Torque Converter/Oil Cooler Cleaner
307-F011 (014-00028) or equivalent
Removal
Raise the vehicle on a hoist; refer to Section 100-02 .
If equipped, remove the drain plug to allow the fluid to drain.
CAUTION: When replacing the transmission fluid and filter and seal assembly; the torque converter should be drained transmission cooler, cooler lines, and cooler bypass valve must be thoroughly flushed to remove any contamination.
NOTE: Do not discard the gasket unless damaged. This is a reusable gasket.
Remove the transmission fluid pan and gasket.
Loosen, but do not remove the bolts.
Remove the front and side bolts.
Lower the front of the fluid pan and allow the fluid to drain.
Remove the remaining fluid pan bolts and the fluid pan.
NOTE: After removal, discard the filter and seal assembly.
Remove the filter and seal assembly by carefully pulling and rotating the filter as necessary.
CAUTION: Be careful not to scratch or damage the aluminum bore. The new seal may leak and damage to the case will result.
If the seal remains in the pump bore, remove it carefully with a small screwdriver so as not to scratch or damage the aluminum bore.
Remove the torque converter drain plug cover.
Remove the torque converter drain plug.
NOTE: If equipped with a radiator in-tank transmission fluid cooler (5.4L) and an oil-to-air (OTA) the in-tank fluid cooler will need to be flushed, and the OTA will need to be replaced.
NOTE: If performing the drain and refill procedure for maintenance the oil to air oil cooler will not need to be replaced. If performing an overhaul the oil-to-air cooler (OTA) will be required to be replaced.
Thoroughly flush the cooler lines and the cooler bypass valve.
Installation
After the torque converter has drained, install the drain plug.
Install the torque converter drain plug cover.
NOTE: Prior to installation, lightly lubricate the seal with clean Motorcraft MERCON® Multi-Purpose Automatic Transmission Fluid XT-2-QDX or MERCON® equivalent.
Press a new fluid filter and seal assembly into the pump bore until seated.
CAUTION: Mixing (A) 4x2-style and (B) 4x4-style transmission fluid filters and transmission pan assembly components can cause transmission damage.
Install filter assembly and transmission pan.
NOTE: Transmission pan gasket is reuseable unless damaged.
NOTE: Apply a light coat of petroleum jelly to hold the gasket to the fluid pan.
Position the (A) gasket onto the cleaned fluid pan. Make sure the (B) magnet is positioned over the dimple in the fluid pan.
Install the fluid pan.
Position the fluid pan.
Install the bolts.
Lower the vehicle.
CAUTION: Use only Motorcraft MERCON® Multi-Purpose Automatic Transmission Fluid XT-2-QDX or MERCON® equivalent. The use of any other fluids can result in the transmission failing to operate in a normal manner or failure.
Refill the transmission (7003).
Add 6.2 liters (6.5 quarts) of MERCON® or MERCON® equivalent transmission fluid to the transmission through the fluid filler tube.
Start the engine. Move the transmission range selector lever through all the gear ranges.
Check and adjust the transmission fluid, in 0.24-liter (0.5-pint) increments, to the proper level (cross-hatched area of the fluid level indicator (7A020) ) at normal operating temperature.
SECTION 308-07B: Transfer Case 1998 Expedition/Navigator Workshop Manual
GENERAL PROCEDURES
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Transfer Case Draining and Filling
CAUTION: If the proper fill procedures are not followed, transfer case failure can result.
NOTE: Fluid level must be just below the fill plug.
Remove the fill plug from the rear of the transfer case, and check fluid level.
If the fluid is below the level, fill with Motorcraft MERCON® Automatic Transmission Fluid XT-2-QDX or -DDX or MERCON® equivalent.