That might be doable, but the map might get messy.
The basic run-down is..
Jenquai have weak shields and armor, but are stealthy (in EnB, low "sig" makes them hard to see, in SE4, only Jenpie will have cloak, same as in EnB), average speed and a choice of hard-hitting but slow-firing beams, or near-equivalent faster firing beams that do less damage per hit. They also have summon and fold space skills, which can be used to move them or their enemies around on the battlefield (Jenpie may have exclusive access to tractor/repulsor technology, but even if non-unique theirs will be greatly enhanced). In EnB, Jenquai also tend to have good resistance to damage to mitigate their shields and armor problems (Jenpie in SE4 may have more advanced emissive armor).
The Progen are opposites of the Jenquai (and they hate them, too), with strong shields and armor but suffering in the speed department (if your motto is "speed is life"--don't be a Progen). The Progen prefer projectile weapons, which fire much faster than beams and missiles but do less damage per hit. This may turn out to be a great disadvantage in SE4 as I've heard combat is often resolved with the first salvo later on in the game. In EnB, the Progen are supposed to be the ultimate warriors, and get an extra weapon slot over their counterparts. I'm most interesting in emulating Progen "Shield Nova" which, while draining the Progen's shields, strikes every enemy in range with energy damage. Don't know how this would be done in SE4, however. Failing that, the Progen have a skill that allows them to slow their (almost always faster) enemies down, thus Progen may receive exclusive access to engine-disablers, and possibly weapons that in addition to normal damage, have an engine-disabling effect (if possible?). Engine-disablers in EnB mod will skip shields, just like they did in 1.84.
Terrans are an average of the other two races, with shields and armor in the middle and only a few nifty skills. Terrans are the speed demons of EnB (or they're supposed to be..) thus they will receive the benefits of SE4's Propulsion Experts trait. Terrans prefer missiles, which do a lot of damage but fire very slowly, and occasionally miss more often at range (reducing damage). In SE4, facing doesn't matter, but in EnB the ability to fire backwards was limited to missiles (guess the Progen and Jenquai never developped turrets). Terrans would also get the natural merchants trait. Everyone knows Terrans are greedy. Being the only race with the Hacking skill, Terrans in SE4 will get exclusive access to the computer virus. That's all I can think of for Terrans off the top of my head, aside from some skills I don't want to emulate.
Weapons tech will not be exclusive up to a point. Each race will be able to research the others' preferred weapons, but will not be able to research it to the highest level. This mod will require much playtesting to get the weapons balanced I think.