ランタイム時に may not be that bad, but feels awkward as you guessed.
And Japanese ランタイム as a noun tends to mean "runtime library" (such as JRE, .NET Framework) rather than "run time". For example, "Javaランタイムをダウンロードしてインストールしてください".
The normal way to say "at runtime" in that context would be (プログラム)起動中に, 実行時に, etc.
The word modulo is read モジュロ, while the abbreviation mod is read モッド. In many programming languages, the modulo operator is written with a symbol such as %, but it still represents either modulo or mod, so you could read the symbol either way.
Written form Reading
x modulo y x モジュロ y
x mod y ...
There's one I can't find much about, but I think I've determined the basis for most of your list. Here it is, regrouped a bit:
ほげ - hoge
ほげら - hogera
ほげほげ - hogehoge
ふが - fuga
ぴよ - piyo
The first three are all variations on hoge. Digging around, this appears to derive from the verb hogeru, "a hole opens up, a hole appears; to fall apart". ...
[programming] tag, BNF
fundamental rule(s) of a Japanese sentence
This (below) seems pretty good. If there's a similar version (rules for Jp sentence) in English, i'd like to see it.
（１） 文 ＝ （連用句）＋（体言句）＋ 用言句
（２） 用言句 ＝（連用句）＋