I just went through the same thing and swapped in the ZF5 instead of suffering with the E4DOA any longer. I highly recomment it if you like driving stick shifts. I am very very pleased with the swap and would rate it in the top 3 improvements I have made to the truck.
Right up there with the turbo.
I have experienced a large increase in fuel mileage also after the swap. I think it alone would pay for the swap in time. I went from 15 to 20 mpg on the last tank full. I havent towed anything yet to give the towing improvement but I bet it will be huge also due to the E40 changing gears on me at random speeds.
Hopefully this helps,
Eric