Tool-like bass sound

All Tools songs are in drop d except for prison sex which is in b or maybe drop a. That helps I reckon, you won't get the same punch tuned lower. The Karnivool guy does do a good Tool impression with his fingers though
 
It might seem obvious, but brand new strings really help a lot, to get that steely, bright sound. I don't know what strings Justin Chancellor uses, but I've found D'Addario ProSteels are great for getting that kind of tone and keeping it a lot longer than with other strings.
 
prison sex is in D, parabola is in B-E as was stated. undertow (and everything prior) was the old bassist. (tool megafanboy all through high school.)

also was always obsessive with tim's bass tone... he too does the a/b/y clean/dirty stack. i forget any details beyond that.

oh and...the intro to tool - flood, i'm pretty sure, is just a rat pedal.