Nothing effects them outside the number of them and the max tonnage of the Mech.
There are several different types of Jump Jets, but they are locked in based on your tonnage. And by that I mean if you are in a Mech that has a max tonnage of 50, it will use Mk. 4's. No matter what you have the tonnage of your Mech at, it will only use the ones the Max weight falls within. Each Jump Jet has a specific power rating, it's labeled as boost_z within the variables. The higher the Mk. number, the weaker the Jump Jet. So a Mk. 3 is weaker than a Mk.1.
Edited by Norris J Packard, 15 January 2013 - 11:36 PM.