I'm sure there are others who may give better advice or another avenue to look at. Since you said the fluid looked really dark, I would think the fluid is burnt and has lost most of its ability to do it job. Possible the transmission pan has a lot of metal dust (filings) mixed in the fluid and is plugging the filter and causing the transmission to act like it is low in fluid. I would start with the simplest cheapest solution of changing the transmission gasket and fluid in the pan.
If the jeep starts and runs without shifting in neutral, then I would have a transmission fluid exchange done. This will remove all the burnt fluid and replace it with fresh fluid. If the filter change does not work, then It may need towed to a transmission shop to have the bands checked to looseness and adjustment. Good luck..