Stepconfig wont set up tandem y axis limit and home?

I am trying to set up a xyyz and when I do the stepconfig it wont set up a input limit switch y2 on my joint 2, even though I set up the input as tamdem y limit and home, it sets the hal as "a" limit and home. and it also it doesnt set up my z limit and home, in the hal it shows up as u limit and home?  Am I missing something? or does this need to be modified in the hal with an editor? 

At the very start did you choose XYZ or XYZA machine?
Choose XYZ.
You can also manualy edit the hal and ini files, but requires a bit of attention, although LinuxCNC is very good at pointing what is wrong.

Sounds like you may be using 2.7 or lower.
Please use the 2.9.3 ISO on the downloads page.