His tone on ToT is a dark growly SOB. The drums take up all the very low frequencies so basically cut those out from your eq, boost the low mids a tad, roll treble down to your liking, and pluck near the bridge. Thts what works for me when i try to cop a tone like that. Probably my fave JMX tone next to his Images and Words tone.
On FII he seems to hae a bit of dirt in his tone, and low action. JMX is a hard plucker so a lot of what you hear is him striking the strings.
I bongo, you bongo, he she me....bongo?