I too have had my issues with the e4od in my 90 e350, so have grown to know a little about the trans and how it operates. Most all of the problems associated with this gearbox are related to the sensors and electronic controls. Bad grounds are also a common problem that cause many failures for this system as well.
The MLPS (manual lever positon sensor)has been known to cause a great deal of problems one of which is the "Nagging Netural" problem. The trans will shift into a neutral condition due to improper signal from the MLPS. Sounds like you might just have this issue. Another common problem is the FIPL (also known as the TPS)throwing bad signals about the position of the throttle and this will cause a fault light when everything seems to be running just fine. Both of these sensors can be easily replaced at relatively low cost.
You need to get the codes read from the computer. A code reader for your veh is only about $30 and these will guide your efforts. The
ford truck enthusiast site has a forum on trans problems that you can get information from as well.
Good luck