The claim that "my eyes and heart will always be there" appears to mean nothing more to me than the fact that the LORD would pay special attention to the temple and have a special affinity for it; the LORD would reveal Himself to His people through the temple.
Stephen's speech in Acts merely highlights the transcendence of God.
Put simply, if you put these together you arrive at the following truth - God is transcendent, yet He reveals Himself where He will.