√YOD “fence, enclose”
This root appears in a discussion of the possible origin of Sindarin -ion² “-land”, blended with the root √YON² “wide, extensive” (PE17/43). A more common variation of the latter root was √YAN¹, making the status of √YOD uncertain. The derivatives of √YOD are similar to those of √(G)LAN from the late 1960s, which presents a more complete paradigm.
√YON “son”
This root was the basis for Elvish “son” words for much of Tolkien’s life. The earliest indications of this root are ᴱQ. †Y̯ó (or y̯ond-) “son” and ᴱQ. yondo “male descendant”, both tied to the patronymic suffix ᴱQ. -ion “son of, descendent of” appearing in many names (QL/106). In the contemporaneous Gnomish Lexicon there was also the related patronymic prefix G. go- (GL/40), which implies the existence of a root *ᴱ√YO(NO) since initial [j] usually became [g] in Gnomish. However, go- was deleted and changed to G. bo-, along with new Qenya forms ᴱQ. vô and ᴱQ. vondo (GL/23, 40), implying a change to a root *ᴱ√VO(NO).
In Early Noldorin Word-lists from the 1920s, ᴱN. gô “son” reappeared along with ᴱQ. ion and yondi (PE13/144). In The Etymologies of the 1930s the root appeared as ᴹ√YŌ or ᴹ√YON “son” with derivatives like ᴹQ. yondo/N. ionn “son” and patronymic -ion (Ety/YŌ). However, in notes labeled “Changes affecting Silmarillion nomenclature” from the late 1950s, Tolkien wrote “Delete entirely yondo = ‘son’! Very unsuitable” (PE17/43). This particular note was rejected when Tolkien changed √YON² “wide, extensive” to √YAN¹ (PE17/42). Other notes in the same bundle indicate Tolkien was still seeking a new word for son, saying “Q wanted: son, daughter”, though yon(do) remained among the forms he was considering (PE17/170, 190).
However, it seems Tolkien eventually stopped vacillating and restored √YON, since the patronymic -ion was never discarded, and yon- was the basis for “son” words in notes from the late 1960s (VT47/26).
√YU “both, [ᴹ√] two”
This Elvish root was connected to the sense “two” or “both” throughout Tolkien’s life. The first clear manifestation of this root was ᴱQ. yú “twice” and ᴱQ. yúyo “two” from the Early Qenya Grammar of the 1920s (PE14/49-51, 82-84). The root ᴹ√YŪ “two, both” appeared in The Etymologies of the 1930s with derivatives like ᴹQ. yúyo “both” and ᴹQ. yúkale/N. uial “twilight” (Ety/KAL, YŪ). The root √YU appeared several times in Tolkien’s later writings, generally with the sense “both” (PE17/70; PE21/74; VT48/8, 10). It was likely related to the ancient dual suffix ✶-ū.
√YUL “drink”
A root meaning “drink” in Tolkien’s later writings, most notably the basis for the Q. yulda “draught” and Q. yulma “cup” from the Q. Namárië poem (LotR/377). It seems likely the root was coined in association with this poem, though there are no signs of any yul- forms in its earliest drafts from the 1940s (TI/284). The root √YUL (or √JULU) was mentioned a number of times in Tolkien’s later writings in the 1950s and 60s (PE17/63, 180; PE22/155; WJ/416), but there is no sign of it before then. In earlier writings Tolkien generally used √SOK or √SUK for “drink”, and the root √SOK appeared as late as the Quendi and Eldar essay of 1959-60 (VT39/11), an essay that also referenced √YUL (WJ/416). Thus it isn’t clear whether √SOK was supplanted by √YUL, or if the two roots coexisted.
ᴹ√YUL “smoulder”
A root in The Etymologies of the 1930s glossed “smoulder” with derivatives like ᴹQ. yúla/N. iûl “ember(s)” and ᴹQ. yulma/N. iolf “brand” (Ety/YUL). In all likelihood it was supplanted by the later root √YUL “drink”.
Neo-Eldarin: For purposes of Neo-Eldarin, I’d recommend positing a Neo-Root √YOL “smoulder”, which could salvage the Noldorin derivatives of this root. This doesn’t clash with (Neo-)Sindarin derivatives of √YUL “drink”, since in Sindarin the initial yu- became the (vowel) y, as in S. ylf “drinking-vessel” (WJ/416).
ᴹ√YUR “run”
A root in The Etymologies of the 1930s glossed “run” with derivatives like ON. yur- “run” and N. iôr “course” (Ety/YUR). It was a later iteration of ᴱ√ẎURU “run” from the Qenya Lexicon of the 1910s with derivatives like ᴱQ. yuro “a run, race” and ᴱQ. yuru- “run” (QL/106). For purposes of Neo-Eldarin, it is probably better to stick to the better attested root √NOR.