In my opinion, the 58 Les Paul is Mark's best guitar.
That blue LP used on Mark/Dylan tour is also great. By the way, for me, 2011 was the last year that i hear MK playing intense guitar.
As a guitar player, i always say that thr amplifier is THE key for a great tone. I tend to affirm that the amplifier is 70% against 30% of guitar.
The Bia album has a great tone, but i believe that Neil Dorfsman has a big influence on that tones.
During the BIA Tour, i believe Mark used a 120w Mesa Boogie Head with a 4x12 Celestion Speakers and a BB rack. It was a big, compressed and processed sound.
For me, the Shangi-la album have the best Les Paul tone of Mark's albuns ever.
Funny thing is that i generally dislike a big part of Mark's guitar tones, expecially during his shows.
The worst tones from Mark was the MM Tour and the Tracker Tour.
His bests strats are the Whites ones. The 65' and the 85' (The Bug Strat)
Sorry my poor english.