Sounds like a couple of layers of stuff going on. But the most noticeable thing to me is that there is some guitar stuff going through a rotating Leslie speaker
Shields has said he put pretty much everything on that album through an Eventide Harmonizer, which was an early studio multieffect unit. You could create a lot of unique sounds with one of those by playing with the parameters to make it do stuff it wasn't supposed to be doing, and he spent a lot of very expensive studio time tweaked out of his mind doing just that. He's also fond of manipulating the trem arm on his Jazzmaster while he plays to get that distinct warble, but you probably knew that.
Trying to figure out exactly what Kevin Shields is doing is one of the great mysteries of this world.
It's not very high quality (such is the fate of the youtube link), but it'll give you a decent Idea. Yeah, I knew about the Eventide, but I don't really have the time to sit down with one (assuming I could find one, etc.) and spend days trying to come up with a third album... Right, but this is also a "how can I approximate this tone" thread in a disguise. Would you like to see the disguise? Ok, here it is:
A GigFX Chopper would do the modulation straight out of the box. All I hear is a tremolo with varying speed post distortion on one guitar, the other has multiple harmonies going with a lot of gain. So yeah, if I built a pedal board around making that sound with a single instrument, it'd go: Inst >> Splitter A >> distortion >> GigFX Chopper >> amp B >> EHX POG >> clean boost >> amp Also, Eventide Harmonizers are still the best rack unit multi-effects out there, and hands down the best harmonizers ever built.
he used TWO(2) boss pn2s and a marshall shredmaster for distortion. i love the pn2 i have one. id like to have 2. or 50.............