It was lots of work swapping in the E4OD but I'd never go back to a C6.
You'll need a transmission that is 1989-1991 model year. That way, you can still have the mechanical driven speedometer setup. Alternatively, you can get a later model transmission (1995 and up are much better built) and then swap the tailshaft and extension housing...this does require a full rebuild but this is recommended anyway, when using a 2nd hand unit.
Some have been able to make the ford OEM control electronics work in an older truck by swapping everything out. It could be a cheaper option, if you can find a good donor truck. But the system has more sensor inputs and may come with more gremlins to chase down. Personally, I'd go with the aftermarket controller, even though you pay more up front.
My biggest warning to you is this: Early E4ODs are mechanically unreliable. To build one right requires lots of upgrades. Once the factory recommended updates are done, it will hold up as well as anything else out there (yes, including a C6).
Even though it was expensive and time consuming, I consider the E4OD upgrade to be the single best mod to my truck over the years. More than turbocharging and more than converting to 4wd.
