Chita חיטה - "wheat" also has a fairly simple explanation. Klein points out that it probably derives from the root חנט, meaning "to ripen" (with a dropped nun). And we've already discussed shibolet shual שבולת שועל - "oats" and shifon שיפון - "rye" (at least according to their use in modern Hebrew.) What's left? Kusemet כוסמת.
As with shibolet shual and shifon, the identity of kusemet isn't clear. The word appears in the Bible (Shemot 9:32, Yeshayahu 28:25, Yechezkel 4:9) and in the Talmudic literature. The medieval rabbis generally identified it as spelt, but the current scholarly opinion is that it was more likely emmer wheat (unlike emmer, spelt has not been found in Egypt and the Land of Israel in archeological excavations of biblical sites). The name probably comes from the root כסם - "to shear, clip", and "the names derives from the short hairs of the ears which look as though they have been cut" (Encyclopedia Judaica, "Wheat"). However, with kusemet there's an added twist: in Modern Hebrew the word means "buckwheat". Unlike shibolet shual and shifon, there's no halachic opinion that buckwheat is one of the five grains (with all of the laws relating to them). So how did this come to be?
I couldn't find any clear answers, but after a lot of research, I believe I have a possible theory.
First of all, it's important to note that this wasn't an invention of Ben Yehuda. In fact, his dictionary doesn't mention the identification of kusemet with buckwheat at all (even to reject it). I did find it in three different sources from 19th century Haskala writers. Mendele Mocher Sfarim in 1862 (Toldot HaTeva) and Moshe Studentzky in 1853 (Orchot Chaim) both use the word kusemet as buckwheat in “scientific” definitions, as well as an earlier use by a Jewish convert to Christianity, Aaron Pick, in 1845. I have no reason to believe they were all influenced by one common contemporary source - and if it exists, I couldn't find it.
So I think it was probably more likely that these various sources were all inspired by common usage (Jewish or non-Jewish). Here the trail goes cold, but I think there are certain hints about what might have led them to this translation.
If we go all the way back to the Latin Vulgate translation of the Bible, we see that kusemet was translated as "far". Interestingly, far, at the time, could mean either spelt or emmer (the confusion continues to this day). But later, far came to mean grain in general. The Vulgate was the main influence for pre-Lutheran bibles, written in Low German, which weren't known for their scholarship. Some of them translated kusemet as boekwete, the German word for buckwheat. (Luther translated kusemet as spelt, and his translation became the standard in Germany after his Reformation, and supplanted those earlier bibles.)
Low German is closely related to Dutch, and here we get a few more clues. There are two legends in Holland about buckwheat. One is that buckwheat was first brought to Europe from the Holy Land by Joos van Ghistele in 1485, and the other is a folk etymology mentioned in a number of sources, such as Bert Greene in The Grains Cookbook (page 56):
It was the Dutch who gave buckwheat its rightful name. In 1549 the officially dubbed it boek weit (book wheat) to honor the Scriptures whose auspices, they claimed, brought it to flower on their shores.
Neither of the above is likely true (buckwheat was never found widely in the Land of Israel, and the correct etymology is "beech wheat", since buckwheat seeds and beech seeds look similar). But that's not terribly relevant to our search - if people in that area thought that buckwheat was a biblical grain from the Holy Land, then it makes sense that when they found a strange word in the Bible, which they understood as just meaning "grain", they would connect the two. And so therefore kusemet could go from far to boekweit, and if this association continued for a few more centuries, then Jews could make buckwheat into kusemet.
And this is apparently what happened, for in addition to the Haskala sources I found, the Aruch HaShulchan (Orach Chaim 208:181) writes in the 19th century that most people knew that buckwheat was not one of the five grains. The fact that he needed to point that out is a sign that there was already wide use in Europe of kusemet as buckwheat.
As we mentioned, Ben Yehuda made no reference to this usage. And in halachic literature, kusemet continued to refer to spelt. But even heavyweights such as these didn't have control over the living language of Modern Hebrew. And the language seemed to come up with a solution of its own, and a strange on at that. Kusemet continued to be used for buckwheat, but the plural, kusmin כוסמין, was reserved for spelt - and you can actually find the two next to each other in the supermarket, even produced by the same company.
1. See also Igrot Moshe, Yoreh Deah, 2:25 and Kehati's commentary on Hallah 1:1 for more recent halachic responses to the confusion regarding the meanings of kussemet.