@Imlbrown depending on your controller hardware, M669 S1000 may be too high. A hint whether it's too high is to make some complex moves (e.g.. G2, G3 arcs *) ), then call M122 and look whether hiccups are reported, which are lost steps.
*) but long G1 moves are also complex with your kinematics, because rotational actuators behave nonlinear