Hi Brooks. Welcome to the Zone.
I assume you have this wiring diagram?
http://kelinginc.net/KL-5056WiringDB25.pdf
Your motors will run best with 84V PSU and you are supplying 48. This is going to affect performance some.
All microstepping above 10 is wasted and just cuts down on how fast the motors turn.
set micro stepping to 8 and adjust steps per inch accordingly to about 8000 if you're using ball screws.
If you have the acceleration set too high, motors will stall early.
Steppers DO run hot, but motors will get hot fast if Amp settings are too high. Looks like the 425s should be set for 2.7A, and the N34 for 4.3A.
X3s can have really rough gibbs/ways. Have you at least smoothed up the gibbs? Are the gibbs adjusted properly and not too tight?
You may be experiencing mid band resonance. To correct that, you either have to install dampners or get Geckos.
I'm sure the option didn't exist when you bought your electronics, but nowadays for the same money you could have a g540 with 381s and a 906 N34. That would give you super-easy installation and much greater performance.
CR.