I listened to SMiLE to-day as part of my new listening schedule, and I thought the ascending and descending phrases at the beginning of "Mrs. O'Leary's Cow" would be pretty easy to figure out. I was surprised to find that they're actually chromatic and that - while some instruments modulate up a fourth - the organ phrase remains the same.
I used only guitar and organ, but I think the guitar part is also played on piano and bass.
An-other thing I noticed when I listened to SMiLE about a week ago is that there's contrary motion among some instruments at the beginning of "Mrs. O'Leary's Cow." The guitar and piano go down and then up while what I think is an organ (it's organ in the 1966 version at least) goes up and then down. It results in a kind of musical pulling apart that's kind of unsettling, which actually works pretty well in imparting a sense of the apocalyptic fire.