The tf727 (ihc t-407) automatic transmission that you have in your Scout has a vent hole location that will definitely allow water and mud to enter the transmission and contaminate the atf when submerged. As you can imagine, such contamination is bad news. My recommendation is to cease driving this vehicle until at least some basic transmission service can be performed.
This service should consist of: removing the pan bolts to allow the fluid to drain (probably long overdue anyway). Be advised this will be a messy process. Remove the inspection/dust cover from the bottom front of the transmission. Determine whether or not the torque converter has a drain plug which will be a small, square head bolt. If it does, rotate the engine until the plug is at the bottom. Remove the plug to drain the converter. Once the fluid has drained, remove the filter, discard and install a new filter. Note the color and smell of the fluid. Atf should be red in color and not smell burnt.
Strawberry milkshake consistency indicates water contamination. Dark nearly black fluid that smells cooked means the transmission has overheated. Observe the inside of the pan for an overabundance of metal shavings and/or organic friction materials. A small amount of either is normal and no cause for alarm. A big pile of either indicates component failure. In this event, the unit should be removed from the vehicle for a complete teardown, inspection, and overhaul.
Perform a band adjustment to both the low/reverse band and the kickdown band as outlined elsewhere in this transmission tech section and in the cts service manual.
Reinstall the pan with a new pan gasket. Tighten the bolts according to specified torque value in a criss-cross fashion. Do not over-tighten.
Re-fill the transmission with the proper amount of dexron atf. Do not overfill. Check fluid level with vehicle idling at full operating temperature in neutral, not park on a level surface. Cross your fingers and hope for the best, as the above steps are the cheap, band-aid approach. Some functionality May be restored.
Avoid deep water crossings or submersion in muddy water, unless you block the original vent hole location and relocate it in the manner prescribed elsewhere in this tech section. The unit must be vented to the atmosphere. Simply blocking the hole without relocating it is not advised.
If the fluid is badly contaminated, there's no way to adequately remove all the contamination without a tear down and thorough cleaning of all components, especially the valve body. Might as well perform an overhaul at that point. The torque converter would also be replaced as part of the overhaul as there is no way to adequately flush one without cutting it in half.