Notice
I've tried to transcibe some of the minor parts as well - there is heaps and heaps of overdubbing on this album, the wall of fuzz is laid on thick. Word is, Ministry were touring with 7 guitarists onstage at one time...
There are a couple of /tiny/ variations in the lead line, which I have not transcribed (it would make the print-out WAAY long - and it's already hyooge).
In section K- (the progression with a polyrhythmic prolation), it "sounds" as though there are hundreds of guitars playing at once. Although there are quite a number of overdubs (same as the rest of the recording), This effect is achieved by adding Phase effect (along with delay etc) over the summed bus (all of the guitars).
(That would make it a progression with a polyrhythmic prolation and phase - P.P.P.P. !)
The first staff is dedicated to the riffing bass. This bass has something of a guitarish tone, with plenty of mids (EQ).
The second staff is dedicated to the 2nd bass line. This includes both the "Absolute fuzz", which is a heavily fuzz-boxed bass, with little bottom end, and a "basso profundo", which tends to blend with the kick drum, and has an EQ with lots of bottom end, with the upper mids reduced somewhat. The basso profundo line possibly has blended clean and distorted tones.
In certain sections, the basso profundo line moves to the 1st staff, to double the "main" bass line.
The third staff is dedicated to the guitar overdub that almost precisely mimics the bassline, rather than following the "tenor" guitar lines.
Note that during section K (P.P.P.P.), the bass is in 3/4 against the guitar's 4/4. Play through the requisite number of times, and both lines will match up again.