This is a wonderful piece, hopefully you won't get tired of hearing that.
I have to admit that the fifths at around :40 are a little funny to my ears, but I know that was the practice.
It's really relaxing, well, the organ is a beautiful instrument, I must write for it more, as for sacred music, well I love listening to it, but again, I've only written one piece... well, more will come in time!
Where you testing the stops from the start to .15?

To answer your question, on this particular pipe organ there are two manuals, however there are three divisions of pipes: Great, Swell, and Antiphone. The way Antiphone works is there is a switch that puts it on either the Swell manual or the Great manual, so I don't remember which exactly, but I had it set to the wrong manual which caused me to have to switch the stop right there. I am now playing at a different church with a pipe organ that is a lot harder to record because of its size and foundation, so I haven't yet been able to re record it again with that fix.

Man, that sounds pretty complicated, the most complex organ I play has one manual, no pedals and four stops.
How does one record an organ, I mean, it's not going to be as simple as a piano, that's for sure, how many microphones would you use? Hopefully I'm not being too inquisitive.

Believe it or not for this piece and the previous piece "A Grand Flight" I recorded it with my computer microphone alone, I am sure you notice the quality isn't that good however that particular organ was designed specifically to fit the acoustics of that church which makes it sound great and listenable (I hope) in the recording. To make a quality recording would require me to spend almost $800 dollars in equipment. It needs a lot of microphones both near the pipes and far away from the pipes.

Yikes! that's quite a bit of money. The quality isn't too bad, I assumed you just compressed it to a low~ish quality .mp3 to upload it quickly.
But anyway, the recording is secondary, it's still a beautiful piece!