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Ford now recommends using Mercon V in the E4OD transmission, hence the reason they stopped producing III... But its common knowledge around here that Mercon V doesn't jive well with the E4OD. I've seen many a thread about guys who put V in their E4OD and soon after had to rebuild their transmissions.
The main difference between the two is that the V has friction modifiers which allow the torque converter to slip, effectively reducing TC chatter... Or so they say... Instead it just causes problems with the torque converter SLIPPING and failing...
Because of the shortage of III, lots of guys have stocked up, in case it gets hard to get your hands on later. Thus far I've had no problem finding Mercon/Dextron III, as of about 3 weeks ago. I recommend not using Mercon V unless you absolutely have to.