I think that no one can give you a clear answer to the question at this time, because all of the words, ひ, ひる, よ, and よる have existed for a very very long time. It's just too difficult for present people to find out the origin of the four words.
As far as I know, the words ひる, よ and よる were already common words for daily use in the Heian period (794 - 1185). I think I can say so because emakimono (絵巻物) written in the Heian period contain those words, and they are used in writings which describe their daily life or something not special. For example, all of the three words are used in Genji Monogatari Emaki(源氏物語絵巻). And other emakimono, such as Shigisan Engi Emaki (信貴山縁起絵巻) etc, contain some of them. The words were used as a word or a part of a compound word such as ひるつかた, みじかよ etc. (Those words which I saw were written in hiragana in the emakimono).
The word ひ meaning "daytime" (not the word ひ meaning sun, date, time or weather here) seems to be used in The Tale of the Heike (平家物語) and Kojiki (古事記). (I've not seen the reliable photos of them, so I don't know what character is actually used for the word in them.)
All of the words ひ, ひる, よ and よる are kunyomi (訓読み). And they all were born in the old enough time we can't (or almost can't) trace the origins now. Thus, it is very difficult to find out which word was born first and their grammatical compositions.
There is another Japanese word, Kami (神), which also already existed and was used by Japanese people in the 8th century and is commonly used now. Kami is actually very different from God, but Kami is generally translated as God in English. Anyway, Kami has been one of very important words for many Japanese people, maybe somewhat like the word God in English. So, not a few people have seriously and diligently researched the origin of the word Kami for a very long time. However, no one has succeeded in finding the perfect answer so far. A convincing view on it still doesn't exist. So, we don't know the origin of the Japanese word Kami etymologically. I guess that finding the origin of the る in ひる or よる is more difficult than finding the origin of the word Kami, because they are more ordinary words.
About which word is first, a Japanese linguist, Susumu Ōno (大野晋), wrote an interesting thing in a book called 『日本人の神』.
カミ(神)という言葉は万葉仮名では[伽未]{か・み}・[柯微]{か・み}・[可尾]{か・み}・[可味]{か・み}などと書く。ところが熟語になると形が変わって、「カム」となっている。
[歌牟鵝可梨]{か・む・が・か・り}(神がかり) (神代紀上)
[伽牟伽筮能]{か・む・か・ぜ・の}(神風の = 伊勢にかかる[枕詞]{まくら・ことば}) (書記歌謡八)
このように、カミ(神)のミはカミだけの独立語では mï 。カミを含む熟語では mu である。
こういう場合、言語学的には一般に熟語の方が古形である。例えば、こがくれ(木隠れ)、こかげ(木陰)、こがらし(木枯らし)、こだち(木立)、このは(木の葉)を、独立形のキ(木)と比較すると、キの方が新形である。
I don't know if this is true or not, but, according to his this knowledge, it might be possible that ひる was an older word than ひ and よる was an older word than よ if the words ひる and よる were composed of multiple words. Of course, it can't be certain (at least for now), though.