As you say, Jesus in his divine nature is present everywhere at all times as are God the Father and God the Holy Spirit. Since the incarnation, Jesus also has a human nature composed of soul and body. Jesus in his human nature is not present everywhere but only where his body and soul are just as we are not present everywhere but at that location where our body and soul are presently. Since his resurrection when Jesus united his human soul back to his body and subsequently ascended into heaven, Jesus is wholly present in his human nature, body and soul, where ever his body and soul are at and they do not become separated as when Jesus died on the cross and his human soul as we profess in the Creed descended into hell to free the just there and take them to heaven. And at his resurrection, Jesus united the soul back to his body never again to die and to be separated from each other. The soul is the form of the body and it animates the body.
The great mystery of the eucharist is that Jesus is wholly present in his human nature, body and soul, under both the species of the bread and wine after the consecration at Mass and at the same time and without leaving heaven, Jesus is wholly present body and soul in heaven too. However, Jesus’ true bodily presence is present under the sacrament of the eucharist in a different way than Jesus’ bodily presence in heaven. Without getting into specifics presently, the whole and entire Christ, body, blood, soul, and divinity is truly present under the consecrated elements of the bread and wine invisibly while at the same time Jesus is present in heaven in his body visibly just as he was when he lived and walked on the earth and at his resurrection. The difference is that Jesus’ body and blood in the sacrament and by a completely divine and supernatural miracle are not extended in three dimensional space so we can’t see them or him although his body and blood are truly present, while in heaven Jesus’ body is naturally extended in three dimensional space just as it was when he walked on the earth and when he rose from the dead and just as our own bodies are now and which we can see. It should be noted that the person or soul in a glorified body such as when Jesus rose from the dead has a supernatural power (a gift called clarity) to make their body visible or invisible to human eyes such as when Jesus vanished from the sight of the two disciples on the road to Emmaus during the breaking of the bread. But, this kind of invisibility of the body which remains naturally extended though without color is not the same as the transubstantiation of the bread and wine into the body and blood of Christ in the eucharist and the unextended and invisibility of his body and blood there.