If you have it, you might be able to glean that info from the configuration or parameter info for the original control. (at least the encoder counts/degree or rev.)
Often the encoder's line count is somewhere on its id lable, but you still have to figure out your planetary's reduction (might be in it's model description) and any other reduction from belt or chain cogs.
For a dual motor gantry config, right now it is advisable to use the development branch of Linuxcnc, aka Master (2.8-pre) rather than the general released version (2.7). As it is much better suited to configurations where joints 0,1,2,3... don't necessarily equate to axis x,y,z,a... Such as for a simple duel motor gantry or more complex non-trivial kinematics.
If you use pncconf after you've made any hand edits, it will overwrite them. So, if you must rerun the wizards, backup your old files first.