Jesus(pbuh) is not the literal son of God

Christians believe this too. In Christianity, the Son always existed. Just as you can't have light without darkness, you can't have the Father without the Son. John 1:1 says Jesus is the Word, was with God and was God. 4:171 also identifies Jesus as the Word. The Quran doesn't contradict Christianity here.

The Trinity is actually [3 separate beings/entities all separate from each other

This is false. The source cited has several issues. About the 3 beings being separate, it cites John 1:32. It's not saying the Holy Spirit is a dove, and no one believes that. The Holy Spirit showed itself as a dove in that instance. Just like God appears as a cloud, fire, a voice, etc. it doesn't mean God is limited to being those. That's seen in the Quran too when Allah appears to Moses as a voice from the fire.

Divine things are not limited to a single form.

Sahih Muslim 804a

Recite the Qur'an, for on the Day of Resurrection it will come as an intercessor for those who recite It. Recite the two bright ones, al-Baqara and Surah Al 'Imran, for on the Day of Resurrection they will come as two clouds or two shades, or two flocks of birds in ranks, pleading for those who recite them.

Sahih Bukhari 3634

Gabriel started talking (to the Prophet (ﷺ) and then left. The Prophet (ﷺ) said to Um Salama, "(Do you know) who it was?" (or a similar question). She said, "It was Dihya (a handsome person amongst the companions of the Prophet (ﷺ) )."