installed new servo motor & encoder now getting Y axis error-A2100 control-Tree 750

Well after having the servo and encoder rebuilt on my tree vmc 750 I'm getting a Y axis error:

Error is:
Y axis grid align error
The grid align for the yaxis completed its alignment move without finding the pulse marker

Remedy: check the encoder, encoder wiring, and marker pulse setup. the marker pulse setup is located in the servo configuration axis data. The index invert A and index invert B fields must be set correctly or the marker pulse may be missed.

I understand what it is telling me basically that I will need to "re align" the encoder so to speak but how do I do this? I went into the axis configuration page but it is only taking hard inputs (numbers) where can I find where the triggers are when I move the Y axis to find out how to update this?

I have the manuals for the machine but they are not extremely intuitive...or detailed in some cases. Anyone capable of walking me through this on a Tree vmc750 with A2100 control?

Thanks.