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Pros and cons here are pretty obvious... The E4OD has another gear the C6 doesn't have, but it's also computer controled and more complicated to install in a non factory equiped vehicle. There's no way to say if one is stronger than the other, it depends what vehicle the trannys came from and if they have any updates or performance modifications. Either can be built up to handle just about any power level.
I've had both, and the E40D seems like it doesn't have the "drag" the C6 had. Both had the same engine (only difference is one was MAF and other SD...but both stock). My old bronco with the C6 and 351 was a slug...felt like it had no power at all, but the E40D and 351 in my truck now will flat get up and go, It makes my 4WD truck feel light.
I don't know if it's true or not, but I've heard that there is a company that makes a stand-alone computer to control the transmission only so I guess now you can throw it behind alot more motors now.
The C-6 was originally a big car transmission with high gearing to match. The E4OD is electronically controlled with better gearing for truck useage, i.e. lower first gear than a C-6, and an overdrive gear that the C-6 doesnt have. It depends on the year of E4OD that you are looking at, earlier E4ODs that have never been touched from the factory may need updates to equal the later model E4ODs. Previous owner usage of that tranny is another factor that is a heavy unknown, sometimes the tranny was left pulling or doing heavy work with the overdrive engaged. Doing so often burned the clutches and clutch plates up burning the rest of the tranny up from the debris. But all the autos are sensitive to debris in the tranny.
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