Growing up in God's House -- revision

[Donald Q.]

I looked for him the way some people look for ghosts I think the lead in here is too long for it to all occupy one line, maybe line break after 'for him'
and dread meeting celebrities. I would have 'or' instead of 'and' but that's just minor style point

They said the church was his house,
that he was in the air
all around us, I know you come back to this later in the poem but I feel like in this stanza the sentiment of this line is equally expressed by those before and after it
and we could hear him whisper. Again with the pace/rhythm, I would maybe just have 'that he was in the air,/ that we could hear him whisper' 

I knelt by the altar
like the adults who wept there,
playing make believe. There's a sort of horrible [in a good way] dissonance between the playing and the weeping, I almost feel like there's more to say here

I opened the 6-foot grand piano Love the specificity 
and played from mom's sheet music. Do you need 'sheet'? I am unsure
She told me once that she saw him  Too many words, need a rephrase or perhaps a line break? Or maybe adjust the tenses 'she told me once; she'd seen him'
emerge from the cross
and that it bled electric red.
He asked her if she was ready for heaven—

she asked for more time
to raise her kids, to see us get saved. Keep it personal. 'To raise us, see us saved', keep it laser tight

I never stared directly
at that cross again for fear
of what otherworldly things I might see. Not sure about this stanza; the imagery of the vision has already conveyed how startling it is, I think you can nail this in a single line. Say you never looked again. We know why. 

I climbed the steps to the pulpit  I think the previous two stanzas are the emotional heart of the poem, so now we are zooming back out and reflecting, clearly. It works, but I think three more stanza breaks is one too many perhaps? 
where only one man was allowed to stand. We don't care about the preacher now that we've heard about the mother and the holy son. 'Where one stands alone' or similar would hit harder 
On tiptoes, I looked over the empty pews
and said prayers
through a cold microphone I feel like it would definetly be 'into a' , but that you don't want to repeat yourself in the next line. 'through' feels wrong to me, I think this and the next line need balancing a bit
into the air
all around me. See, here, this works wonders. Now it strikes a lonely chord. 

I looked for him the way people look for funnel clouds 
and dread seeing the dead one day. I like the imagery but this two liner just kills the pace a bit for me, I think bundle it with the next stanza

Was he there, above me
all the time
                       wordless,  these three lines spell it out a bit too much for me, you can say this without saying it - eg with the empty microphone
waiting for me to discover fire  fire?
and finally
earn his love?  

There's some powerful stuff in here that you are doing a good job with. You also are dealing well with the trickiness of having a past tense poem which subsequently contains a flashback (I too enjoy a challenge!) 
Nonetheless I think there's still some nuts and bolts to tighten so that we are completely with you throughout, I think the last two stanzas are a bit away with the faeries at the moment and lack the visceral qualities of those preceding. Stay confident that your imagery can talk for you. Keep going, eager to see a revision. 

Also honoured to have made it to the signature