It's a BIG step, and a misstep, imo. Those miniscule spirits can manifest in some ways, but the omnigod can't? Something is wrong w that step that you suggest.
I never said that God can't manifest Himself. But when He does it, it's always a bigger production. God has manifested Himself to prophets and holy men ever since the world began. And He's always left witnesses. Not only did Moses see Him face to face, but later seventy elders of Israel, and a few others, not only saw Him, they dined in His presence. And the apostles of old were transfigured on the mount with Jesus, Moses, and Elijah, all of whom they saw for an extended time. All of the apostles, with the exception of Judas, also stayed and conversed with Jesus for 40 days off and on after His resurrection. That's a long time to spend with someone who was crucified, then resurrected.
God is omnipotent, but not omnipresent. He is the Father of all spirits, but those who remain behind after death are those who, for whatever reason, don't want to move on until they're ready. I've studied numerous near death experiences and the consistency makes me think that many are telling the truth. For the good, decent, honorable people who move on after death, they find great peace and growth. Those who remain behind can become bitter and morose. But my point is that if atheists are correct in saying that science can answer all questions, there shouldn't be hauntings, for that would suggest that man has an eternal nature. It also is indicative of the fact that we all have our free moral agency, and that even after death, God will not force anyone to move on until they're ready. I also think there are evil spirits that have never lived in mortality. These can mimic children or those who have gone on, which means we have to try all spirits that seek us out and not try to seek them out.
I'll always love science...and astronomy. I'm fascinated by the richness and size of the universe, of black holes and dark matter; however, with all the things that science has revealed, I've never found anything that would lead me to doubt God's existence. In everything, there are those things that act, and those things that are acted upon. That's the whole creative process.