You seem to be straining at reaching the Trinitarian perichoresis in Greek or circumincessio in Latin - the mutual indwelling or interpenetration of the hypostasises of the Trinity within each other (St. John 14.10-11).
The Incarnate Christ is not here through the Holy Ghost, but the eternal Word is, since the Holy Ghost is a hypostasis of the Holy Trinity. Thus the body of Jesus does not become present in our hearts, but the whole divine Trinity does, because we partake of the common divine nature (phusis) by grace (but not the divine essence - ousia).
Jesus' physical body was not there, yet he saw Nathanael.
Jesus being God the Word, and as God, can see and know all things. As man, however, He "only" sees all reality past present and future revealed in God through the beatific vision, which His humanity had from the moment of incarnation.
What you are really objecting to is not transubstantiation, but the multiplication of Christ's physical presence - having Him in both heaven and every Host.
Catholics describe this by saying that the substance of Christ - body, blood, soul, and divinity, rather than being limited to a localized manifestation in His body in heaven (as would be normally expected, and as we exist ourselves), is extended in its complete dimensional existence into a manifestation in every Host in the world after the Consecration, and into ever chalice of wine. This is properly a miracle, but certainly not impossible.
The scholastic explanation of St. Thomas is found Pt. III, Q. 76 of the Summa.
http://www.newadvent.org/summa/407600.htm
See especially Article 4.