When the Holy Spirit is referred to in the neuter then the writer is referring to an it. God isn't an it. In the case that the Holy Spirit is a He then that's a reference to God since God is a He. As I originally said, the Holy Spirit is either God or a gift or anointing depending on the grammar and context.John 15:26, is a very good example showing the clear distinction between the Persons, the Father, Jesus Christ and the Holy Spirit:
"When the Helper comes, whom I will send to you from the Father, the Spirit of truth Who comes from the Father, He will testify about Me"
Here we have Jesus Christ speaking in the first-person. He says that He will send the Holy Spirit, "Who Comes from the Father". "from" is the Greek preposition, "para", which is "from the side of", showing that the Holy Spirit is distinct FROM God the Father. Three distinct Persons, Jesus the SENDER, the Holy Spirit Coming FROM THE SIDE OF the Father.
Even though the word "Spirit", is neuter in the Greek, "pneûma", which is purely grammatical, and does not mean the Holy Spirit is "a thing". Jesus does not say "He" here, using the neuter "ekeino", which would agree with the neuter "pneûma". Instead Jesus says, "ekeinos", which is masculine, and used to show a "Person".
In chapter 14, Jesus says of the Holy Spirit;
"16 I will ask the Father, and He will give you another Helper, so that He may be with you forever; 17 the Helper is the Spirit of truth, whom the world cannot receive, because it does not see Him or know Him; but you know Him because He remains with you and will be in you"
Some important points here. Jesus says that the Holy Spirit is "ANOTHER Helper", and uses the Greek adjective, "állos", which means, "One like Myself", and not, "heteron", "different to Himself". The Holy Spirit is ANOTHER PERSON Who is LIKE Jesus Christ. Even "Helper" is in the Greek, "ho paraklētos", in the masculine. The oldest Greek manuscript, the Papyri known as P66 (P. Bodmer II), which has been dated between AD 100-200, has in verse 17, "autón", which is masculine, "HIM", three times. Someone at a later date, has tried to erase the "n" at the send, so that it reads "autó", which is neuter! In John 16:7, Jesus says of the Holy Spirit, "I will send Him to you", where "HIM" is "autón", and not "autó". In verse 18, again we have the masculine "ekeinos" (HE) for the Holy Spirit. The language used by Jesus for the Holy Spirit is very important, as it shows that the Holy Spirit is a PERSON, Who is LIKE Himself, and not "a thing", as some blasphemously teach!
No doubt all of the evidence in the Bible shows, that the Holy Spirit is a Person, Who is LIKE Jesus Christ, and DISTINCT from Himself and the Father, and that the Spirit is also GOD, as the Father and Jesus Christ is.
John 14:17 in the New American Bible and A Faithful Version call the "Spirit of Truth" an it for this reason:
New American Bible
the Spirit of truth, which the world cannot accept, because it neither sees nor knows it. But you know it, because it remains with you, and will be in you.
A Faithful Version
Even the Spirit of the truth, which the world cannot receive because it perceives it not, nor knows it; but you know it because it dwells with you, and shall be within you.
Most of the Bibles are translated under the assumption that the Holy Spirit is a "he" in every context, but as you helped me prove in your post that simply isn't the case. When the "helper" or "comforter" is paired with personal pronouns like "he" then it's just a translation bias.
You can look a bit more into the remote context, beginning with Acts 1:4, where Jesus said the gift they would receive is a Holy Spirit baptism. God Himself isn't a gift we receive, but the anointing or gifts He gives are things we receive.
This is also in the case of Jesus himself who didn't receive his Holy Spirit anointing until John's water baptism.
Acts 10
37You yourselves know what has happened throughout Judea, beginning in Galilee with the baptism that John proclaimed: 38how God anointed Jesus of Nazareth with the Holy Spirit and with power, and how Jesus went around doing good and healing all who were oppressed by the devil, because God was with Him.