to me, a key ingredient here for TOOL is the amp-I have a Dual Rec and 2 Mk IIC+ amps and I am a big fan of the A Jones tone-there is a very crisp ,less compressed sound going on here to me(a lot can be attributed to Chancellor's bass tone and playing as well...)-for me, the MULE wins here -it sounds great with the dropped D tuning-my Rebel Yell is more compressed sounding, so it loses some clarity-the Mule allows for more bite/clarity,especially with the open D riffs/chords that Jones plays higher on the neck-my mark amps are simulclass, and that helps(both el 34 and 6L6)-I have had a Holy Diver , Miracle Man, and Crawler, and I would rank my experience via Tool as follows: 1-Mule(its an AIV) 2. crawler 3. Rebel Yell.....my amps,however, are a big part of this "tonal experiment"
enjoy your quest!