Regarding the Smallstone phaser, JMJ has said in several interviews that he has one that has been modified to go slower than the controls on the front allow - essentially mirroring the effect you get when a battery starts to run out and everything just goes a bit slower. Patrick Geiss is the one who did the modifications. Smallstones can run on batteries and I've run a few down getting a slower effect!
As for the sounds of the various Smallstones, I'm fortunate to own an original 60's orange one, a Sovtek one and newer red version. They do all sound different. The original sounds really gritty, but that's probably due to the electronics being 50 years old! The Sovtek one also sounds a bit gritty and the slowest speeds don't seem as slow as the EHX versions; and the newer model sounds like a lush, cleaner smallstone. They all sound gorgeous really.
Don't forget that for O7-13 JMJ claims to have used the Roland MC303 so it's possible some of the drum sounds came from that.
The rain sound at the end of O7 sounds like white noise rather than a rain sample - that's not to say that maybe he didn't mix both (a la musique concrete). I've used the Roland SH101 to get a pretty much exact sound but in reality, any analogue white noise source will probably do the job. I just find that the 101 has a real sparkle about it, when playing with the white noise. So for JMJ, it's probable that the VCS3 is the culprit as it seems that that's his go-to synth for white noise effects. The ARP 2600 noise generator just doesn't cut it for me on the white noise front - sounds a bit dull.