MDRT is (http://www.marshalljmpmodshop.net/miscellaneous_parts_and_replacement_tubes.htm) Really opens up the dynamics of the unit, IIRC apart from the new transformer there's a component on the tube board that gets replaced (no doubt to handle the higher voltages). However, it does change the tone and some don't do this mod because they prefer the creaminess/smoothness of the original transformer.
The mods probably fall into 2 main categories, mods for different tone(s)/gain etc and mods to fix things eg noise mods because the caps are old, front/rear jack mod for the early units (when they had the line/inst level top switch). Then there are wear and tare mods eg jacks, pots etc.There's also EPROM upgrade, v2.01 was the last and added some dump and load to PC functionality and some more factory presets. The EPROM version is displayed on start up and also on a sticker on top of it (it's near the battery area).