Hey Heavyelement, not sure how much you know about this stuff so please forgive me if you are already across it.
The 3TM mod is the 3 tube mod, ie adding a third tube to the MP1 (and whatever needs to go with it to make it work). Each tube has 2 stages of gain (distortion the way we use them
) as they are twin triode (each triode is a gain stage which boosts the signal at it's input). Stock MP1 has 2 tubes, thus 4 gain stages. 3TM has 3 tubes so 6 gain stages (hence no clean tube sounds anymore). Now more gain = more noise so most 3TM users seem to use noise gates to control it.
The cap changes are changing the old electrolytic capacitors as they have a liquid inside them that goes hard/solid over time and stops working properly. Capacitors are used for a few things but particularly filtering/conditioning the power in the circuit to keep it nice and constant and quiet. When they dry up they don't operate/filter the noise as well thus introduce more noise (very simplified explanation BTW). The noise mod MJMP speaks of is about changing the appropriate components (mostly the old caps) with nice new modern equivalents to reduce the noise as much as possible. This is very important if you do the 3TM mod as the additional gain will boost the noise as well as the signal.