...Thats good news about the SD amp replacement...great. The E Stop problem (soft limit) should be easy to get out of....Hit Reset...Mode Select> 0 (Jog)> 2 then jog off limit.
To Reference xyz ...in Jog Mode1st jog each axis anywhere off the Travel Limits...then type R and then use Jog button "+" ( I think) to start the Homing process for each axis. I do Z 1st...then XY. another thing you might like to do is set your Display to show Axis Lag....hit Mode Select>5 Setup> type TM4 (Lag Display) hit Enter.