Not sure what you mean by how to differentiate between them when researching them.
The earlier 4 cylinders 4000 was made from 1961-1964 and the newer 3 cylinder 4000 was made from 1965-1975.
If you're searching documents on the internet, and if the document doesn't specify which it is, either by the number of cylinders or the year, then you have no idea what they're talking about, although you might be able to get clues from other features that are mentioned, or from pictures if any are included.
In the gasoline varieties, the earlier 4 cylinder 4000 came from the factory with a Marvel Scheiber carburetor and the later 3 cylinder model came with a Holley, but many of both varieties have been replaced over the years by Zenith carbs, so if you find something that mentions a M/S carb then it's almost definitely an earlier 4000 and if it mentions a Holley then it's almost definitely a later 3 cylinder, but if it mentions a Zenith then you can't be sure.
On the diesel versions the earlier 4 cylinder 4000 came with a Roosa Master (now Stanadyne) injection pump and the later 3 cylinder came with a C.A.V. injection pump.
The earlier ones only came with a 4, 5 or 10 speed (S-O-S) transmission and the later ones only came with a 4, 6, 8 or 10 speed transmission, so if it's got a 5 speed it has to be the earlier one, and if it's got a 6 or 8 speed then it has to be later one.
In any pictures that you find look for the following clues, depending on if the pictures show enough of the tractor and enough detail to see any of these features:
The earlier ones had sheet metal that resembled the earlier hundred and '01 series and the later ones had square grill housings.
The earlier ones had rounded axle trumpets and outboard drum brakes and the later ones had square axle trumpets, double reduction rear axle and inboard wet disk pack brakes (Look for a large diameter round section to the axle trumpets for 6 or 8 inches at the ends closest to the center housing and then reducing in size where they change to the square profile).
The earlier ones had an all-in-one manifold with the intake and exhaust on the same side of the engine. The later ones had separate manifolds with the intake on the right side and the exhaust on the left side (relative to when you're sitting on the tractor).
Overall, the 3 cylinder 4000 with the diesel engine is a very reliable workhorse. One thing to look for is whether it has been run with coolant conditioner or not, as those run without the conditioner may have issues with cavitation and may eventually develop pinholes in the cylinder walls. Other than that, just look at the overall condition of the tractor to try to determine if it has been well maintained over the years.
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