when I saw MT in 84 he was playing through two 100 watt Marshall stacks wide open with a series of Boss pedals including a flanger delay chorus EQ (as a boost which was crazy since he was insanely LOUD) and an Ibanez green OD pedal. I looked over his stuff before he hit the stage...I also cannot hear exactly what he is using to shape his tone but I hear a Les Paul up loud enough to compress a bit and some sort of modulation (maybe the flanger set very low).
there is some footage of the MT with Dylan era around...I doubt they focus on his pedals though.