Having done a dozen+ Cummins swaps, several with Ford ZF S6-650's, rebuilt dozens of zf 5 and 6 speeds, built several custom ZF 6 speeds and pieced back together 50+ scattered NV4500's I cannot disagree more with what has been said in this thread.
First off, the gutbag and NV4500 are entirely different animals than the Ford diesel transmissions or the NV5600/G56. The NV4500 and gutbag are wide ratio granny transmissions. They have horrible ratios and shouldn't have ever been considered for use behind a turbodiesel in a truck that works.
The ZF S5-42 and S5-47 diesel versions are close ratio transmissions with ideal ratios for diesel applications that work. Yes, you have one more gear to go through so if you have a light vehicle and want to go fast, say a 12 valve in a flatfender jeep, you may be happy with an NV4500 because the power to weight is so rediculous the engine does not need to be in it's sweet spot to put a smile on your face.
If, on the other hand, you actual use your truck you'll find the close ratios are very nice for not only pulling things and having power whenever you need it, but you can get better economy from the engine because there's less need to wind it out to keep the engine where it likes to be (1600-1800 for Cummins mechanical engines).
The ZF S5-42 has the exact same size shafts, gears and slightly larger bearings than the NV4500 HD dodge diesel version. The light duty gas NV4500 has smaller shafts. The ZF S6-650 6 speed makes both of those look like childs playthings in comparison.
There are two versions of the Ford ZF 6 speed, the 7.3 and 6.0 diesel have different bell patterns. The 7.3 6 speed shares the same pattern as the 7.3 diesel 5 speed, but the depth is not the same hence the reason why Scott had to make two different Cummins plates for the 7.3 diesel pattern. One for the ZF 5 speed and E4OD/4R100 and one for the ZF 6 speed. The difference is the adapter is 1.125" thick for the 5 speed and .5" thick for the 6 speed. You also run different flywheels and clutches for the two and the starter depth changes dpendant on which flywheel you run.
Lastly, the 5 and 6 speed have the nearly the same ratios. The benefit to the 6 speed is it has GRANNY GEAR and a lower reverse ratio, not an extra gear between first and 5th, those are still the same. The Ford 6 speed also has the beautifully well thought out oil pump, cooler and pressure pocket bearing lubrication that no other light duty pickup tranny has. NOTE: The GM ZF6 version did not have this lube hence part of the reason why most GM 6 speeds fail early and GM no longer offers the manual option behind the duramax (because they were too cheap).
The downside to the 6 speed is it weighs a considerable amount, it has a different shift pattern than 5 speeds, it will not fit in anything older than 1998 without cab floor modification and it has a large 24 spline output shaft in 4x4 versions which makes using an older t-case like a 205 more difficult. Not impossible though, if you need a ZF6/NP205 combo PM me.
Probably half done from when I made a 3.5" downpipe fit.
