Yes I got it fixed and it self aligns, I was having a bad problem with it till I scraped the set I was working with and started fresh. I decided that I had set so many switches that I didn't know where the problem was.
When I started fresh and was making sure that every thing was working correctly as I progressed, I found that my homing switches for the gantry "Y" and "A" Were controlling the opposite axis so when "Y" axes stoped it it stopped the "A" axes instead and nothing was working right, It was overshooting the switches, not stopping were I wanted and creating all kinds of problems. I also figured out that once it was fixed that setting the home location from the stop position did not move the gantry it just moves the home position on the table. I was thinking that the gantry would move to the home position after hitting the stops. It doesn't. It does if you hit reference then hit home after it stops at the switches.
Still playing with it now I am down to getting the plasma to fire.
Hope this helps
P.S the slave with master in the general config page does need to be unmarked.