In case somebody finds this page via google or the search forum wanting to know the same thing in years to come; here is Biff's brilliant explanation!
Ok here's a sort of 5th grade science class dissection of the track....
Beginning - Beats from 3 Birdies w/synth noise from same track and Open Up (Remix).
0:52 - This noise is from the remix they did of Leftfield called "open up" which sounds very similar to 3 birdies, essentially the same thing. They sort of alter this sound though the mixing board with echo. Why it is making such a crazy noise at 2:20 is probably because the chems use a synth called the kawaii k4 that has really good filters for rough distortion.
3:00 This noise, which is friggin great, is something they only did live. There is no album versions of this sound. A lot of the chems shows is additions to studio stuff, UnderTheInfluence/ItDoesn'tMatter from this tour right now uses a similar, but not as cool noise. Don't know what synth they are using, it might be a sample of one of their bigger synths they don't take on tour.
Hope this has been moderately helpful. Definitely check out other live shows from 1997 (soulseek is good application) for more stuff like this. There is a show from Atlanta in 1997 that has recently circulated widespread that is a soundboard quality live show with many tracks that have crazy sounds and drums like this one, that was what made the 1997 tour unique.
Best Regards,
Biff
4:00 Claps are from Roland TR-909 drum machine - also a live only addition.