Just briefly on the dilemma...
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A typical example is Filomen 10, where the word "child" in the middle gender is followed by a masculine reference pronoun, which often leads translators to change the meaning of "child" to "son"...
I've looked at the three main "Johannine" texts that Wallace discusses: 14:26; 15:26; and 16:13-14. In the standard NT grammar (BDR, 17th edition), little space is devoted to this phenomenon §296 and point 3) where, it says that the relational pronoun, need not correspond to the gender of the relational word (Gal. 4:19).
In the NT-grammar by Hoffmann/Siebenthal, §265 (general information only) and further reference is made to §289e/f where the "attraction of the relational pronoun" is described as follows: "The relational pronoun is often governed not only by the number and gender of the relational word, but also by the casus. One could say that the relational pronoun is "attracted" to the linguistic casus, or here: "straightened"/"assimilated", hence the talk of relational pronoun assimilation".
According to Hoffmann/Siebenthal,the reference pronoun is GOVERNED by the reference word. My understanding is that while the immediate context suggests "disagreement" (incongruence), it is inherently a misunderstanding of the written text. There is no factual incongruence (see BDR §136) - if I can find a matching number, casus or genus. The commentators on these passages seem to be trying to explain the opposite: that the relational pronoun DIRECTS the genus of the relational word (see Philomen 1:10 above), that it therefore determines, e.g., what genus the relational word is to have. But I'll come back to that. First, the three most cited texts in John.
In John 14:26 the reference word "παρακλητος" is masculine, so "εκεινος" is also masculine. As for the spirit, the following statement, "ο πεμψει," is a reference pronoun in the middle gender because it refers to the spirit (in the middle gender). The congruence is preserved.
If John 15:26 speaks of the coming of παρακλητος, then "ον" is masculine because it again refers to the masculine παρακλητος. And then, again, congruence is maintained: the spirit of truth has the subsequent ο (nominative neuter) because it refers to the spirit in the middle gender. Again, the congruence in gender is maintained.
The more complex text is then 16:13-14, but the immediate context of v.7 clarifies the use of the masculine: παρακλητος appears there again in the masculine, so the whole speech from v.8 onwards must be in the masculine. Vv. 13-14 is a repetition of the promise of παρακλητος's arrival in vv. 7 and 8. Again the consistency in gender is maintained.
This solves the problem for me: there is no incongruence in John, that is, the masculine being ascribed to the middle gender. In my view, the masculine gender ascribed to the masculine παρακλητος and the middle gender of πνευμα is retained.
But, if I go back to Philomen 1:10 (or to the example of John 6:9 or Luke 17:31 see BDR §296(3)), then it can be seen that there can be a sort of change of gender: the "child" in the middle gender becomes "son" by means of the masculine relative pronoun. The explanation, however, is very simple: whether Paul describes Onesimus as a child or a son, he is still Onesimus. I don't think anything changes.
I don't want to make light of it, though: the glaring disagreement, e.g. Rev 12:5 "she gave birth to a son (masculinum), (became) male (neutrum) who (masculinum)..." is deliberately written, and I think it has very serious implications theologically. The writer in the vision saw a symbolic "birth" where a "child" is born as it were, but almost immediately the child is a "man" i.e. there will be no repeat of the situation with the birth of Jesus in his bodily form, where 30 years have passed since the birth of the child, into Christ.
A little conclusion: Incongruences of gender in the NT do occur and are significant, but the most cited texts in John 14:26; 15:26; 16:13-14 in support of the Trinity, however, contain a gender correspondence, so the only thing that can be said about these texts is that πνευμα is here identified as παρακλητος, and since παρακλητος, is masculine, then the following clauses that refer to παρακλητος are also masculine, but there is no personification of it grammatically. If πνευμα is spoken of, then, in agreement with this referent, the middle gender is also used (John 14:26).
p.s. As to Foster's question concerning Eph 2:8, I think no problem arises with the disagreement (incongruence) between the genders: the Greek τουτο refers to το δωρον and not to the feminine of "grace" and "faith". Translated, it means "and this is not of us (i.e. grace through faith), but this is the gift of God". Paul emphasizes "gift" of God versus "from us" (see also Rogers and Rogers, New Linquistic and Exegetical Key...).
p.p.s.: Wallace's study is excellent, but it is such a "discussion killer". Personally, I think the center of gravity of explaining that the Holy Spirit is not a person lies in the meaning of the word πνευμα and how it is used for such disparate phenomena as demons, spirit in man, Holy Spirit, or being transported by spirit somewhere that it simply suggests that the word has a common semantic meaning...