Hey DjC, the later EPROM (v2.01) doesn't affect the rear input but I think later MP1s had the rear input at guitar level as no one was really using the rear line level input . V1 MP1s (the very early ones) have a switch on top to change the main outs from line to inst level so you could either plug it into a power amp (line level) or into a guitar amp input (inst level). They also have the rear line level balanced input (which is why it seemed week to you as it is expecting line level (~1volt) not guitar/inst level (millivolts)). The mod (see MJMPs site http://www.marshalljmpmodshop.net/miscellaneous_parts_and_replacement_tubes.htm) replaces the front and rear jack sockets and changes the wiring a little bit so both front and rear inputs are inst (guit) level. I don't think you need to do this on later units ? It's also a good mod to do if the front input jack (which takes all the ware and tare) gets dodgy or if the way you patch your rack (eg with rack tuner before MP1) is easier/better plugging from the back.
The MDRT (again see explanation on MJMPs site) is a re-designed transformer (it's actually 2 transformers together) suitable for the MP1 and MB1. It can accept 120v or 240v (but needs to be wired appropriately for one voltage or the other, though it can have a voltage selector switch if you are changing continents often). The original MP1 transformer wasn't as good as it could have been so along the way, Machinator and some others came up with a better design. MJMP gets a batch of them made from time to time. My mate MikeB put one in his MP1, wow what a difference, really opens up the MP1, like lifting a bit of boxy fog. I have them in both my MB1s and will put them into my recently acquired 2 MP1s soon.