Starting from Showbiz, this is what i know/believe to know:
This rig was a lot simpler.
I am a little lost on the signal routing of his pedals here because there is only that one image and it is very difficult to make out.
Although I think the chain may be something along the lines of:
Pete Cornish: Channel 1 straight to Ampeg SVT II. Channel 2: (This is a rough guess from studying live videos from that time and from that only picture of his board) Boss OC 2 - Boss LS-2 - Boss OS 2 (in one of the loops of the LS-2 which is set to the A+B Mix setting for extra clean blend and stacking or could be set to the A <-> B which is more likely with either the DD3 or Muff in chain B) - Boss DD3 - EHX/Sovtek Green Big Muff pi - Then into his 2nd Ampeg SVT II. The OC-2 could come after the Big Muff here i'm not entirely sure but that confuses me since octaves running into dirt is a typical touch to his sound but maybe at this point he hadn't discovered a solid use for that particular pedal combo. One of the chains also ran into the Korg DTR1 too before hitting one of the Ampegs. I have not found any record of him using the Boss ODB 3 at this time like Wikipedia sates.
He used Bass Collection basses with 40 - 100 gauge strings, as well as an electric double bass for unintended in the studio and sometimes live.
One of his Bass Collection basses (the green one) later had large white spots painted onto the body.
During the next year (2000) Chris would go on to gain some more gear whilst touring for the album. The most notable thing added to his rig was the 2 Marshall DBS heads with Marshall DBS cabs, to replace his Ampegs. Whether he kept his Ampegs or sold them is unknown.
He would also go on to buy the Akai Deep Impact, Line 6 FM4 and the Human Gear Animato (which he purchased when the band was in Japan). During this time he purchased his first few Pedulla Raptures, which I believe was from Manson's guitar shop, since this was around the same time Matt Bellamy was to also purchase his own custom Mansons. Plus if you look on Manson's site they have been selling Pedulla basses there for years. It's one of the only places in the UK you can buy Pedullas. The Sunburst RB4 identical to the one Kaputsport owns and the blue Pedulla Rapture RBJ2 - 4 used in the Plug in Baby video, (which he would later go onto sell on ebay the following year since he preferred the single pickup versions) were used. Early live versions of Plug in Baby were also played on the Deep Impact or Line 6 FM4 with a more squelchy synth sound...
YouTube - ‪Muse - Plug In Baby Live @ Eurockèennes 2000‬‏
The Line 6 FM4 on the attack synth setting was also used for Sunburn live during the verses from this point.
Origin Of Symmetry:
All his new gear was used to record this album. Here is what i believe was done for some of the songs:
New Born - Clean intro - Muff/Animato/Clean used for the riff. If you listen closely you can hear the distortion panned to one side and clean on the other for this part. A great studio effect used for this part of the song i think. Brings out the most in the riff. - Animato w/ high compression/Clean for the verses and guitar solo - Muff/Animato/Clean for the chorus's too along with the panning effect.
Bliss - Muff/Animato/Clean
Hyper Music - Animato/Clean.. although i think live the Muff may be added on the Chorus/Main riff because i can see Chris stepping on a pedal in that position on his board around that era. Although of course, I could be wrong.
Plug in Baby - Now this song has caused me so many questions that are still pretty much left un-answered, but this is some answers i have come to conclude. The recorded version i strongly believe is OC-2 running into the Muff running into the Deep Impact with everything on for when the riff is played, mixed with clean. During the verse I think the Muff is left off, just letting the Impact and OC-2 do the work. For the Chorus and Bridge i think it's just OC-2 into the Muff with clean blend. Now of course i could be wrong and a little debate with Kaputsport has caused me to re-review his live board for the OOS tour, and most carelessly I missed the blindingly obvious signal chain of Deep Impact - DD-3 - Muff - OC-2. It still confuses me however why on earth he would place the OC-2 after the Muff but who knows. Of course as we all know Chris is very secretive of his tone and signal paths and this routing could of been set up for that picture on purpose, but I don't think this is true after thinking about it. Another conclusion I came too on why this could be set up like this is to do with the input gain on the Deep Impact because of course placing the muff in front of it will change the input gain dramatically whether it is on or not. This could be the reason why Plug in Baby sounds different live and never like the studio recorded tone?
Another way the song could have been recorded is indeed with the Deep Impact in front of the muff used for the main riff/verses, with or without the OC-2 depending on the setting of the Deep Impact and whether or not the patch used had an octave. This could also include the FM4 being used after the Muff for the high end wah like sounds. I must confess i do not own a Deep Impact yet but I do plan to in the future. If anyone feels like selling me theirs let me know I would be very interested. I do however own a Korg G5 and have tried a few settings with that and have come close myself using different combinations using the G5, Muff and OC-2. In both Muff before synth/Muff after synth orders I have come close, although i know i will never achieve the full sound until obtaining my own Deep Impact.
On a side note though I do own an Animato that i recently purchased and must say is fantastic, easily my favorite pedal so far.
In terms of the order of his live board for OOS I am not 100% certain but I have an idea. After studying 2 pictures i own of his OOS board, our discussion and from live video's of that time (e.g. Hullaballo) I have come to believe it is something along these lines:
Pete Cornish: Chain 1 - Boss LS-2 set to the A <-> B setting: Chain A: Animato, Chain B: Line 6 FM4 - Marshall DBS.
: Chain 2 - Akai Deep Impact - Boss DD-3 - Big Muff - Boss OC-2 - Korg DTR1 - Finally the signal is split again. One going to a 2nd Marshall DBS and one going to a Marshall B150.
I think his bass goes direct to the P.A. too before hitting his board, so the clean tone is always there, even when he has the Animato on Amp 1 and Muff on chain 2.
For the first part of the OOS tour Chris still had his Green Big Muff on his board. Whether this was used for recording I don't know but later was replaced with the standard black ones.
If you listen to Sunburn Played live (e.g. Hullabaloo) You can hear the filter sweeps going off in the verse with no bass note behind it, this is because he only has Amp 1 (Pete Cornish: Chain 1) on into chain B of the LS-2 (Line 6 FM4 set to Attack Synth). As the verse progresses and the clean bass notes needed to be added in, he turns on Amp 2 (Pete Cornish: Chain 2) with all of the effects in chain 2 bypassed. Finally when distortion is needed for the chorus he steps on the LS-2 switching chain B to chain A, Turning on the Animato.
I know more about other songs and some information post OOS but I could be here for days. I hope I have been of some help and I'll post some more in the future.
This post is not to disagree or argue anyone's opinions or ideas i'm just sharing my own findings, beliefs and first hand experiences.