Hi Todd,
I'm not sure if I fully understand the requirements and task, but I think the simplest method to start off with would be a coordinated motion approach. For example to form a circle in xy an independent x motion (trajectory) as a function of time is created and an independent y motion as a function of time is created. If each servo axis holds it position at the right position at the right time then the circle comes out perfectly. But in another case (like threading) where one axis can not be controlled well, but can be measured well, then it might make sense to attempt to have the other axis move as a function of the somewhat erratic motion of the first axis.
KFLOP is capable of either method, but the first would be simpler and could be accomplished directly with standard GCode. I'd start with that and capture all the encoder data and then determine if something more complex is necessary.
Regards
TK