Tandem y axis for plasma table

I have tried changing step settings and no difference. I noticed that it is running y2 in linuxcnc when i try to home all so i moved it to the fifth axis port on the mesa 7i96 card and changed my config to match as a tandem, thinking that it wasn't outputting but it is doing the same thing still wont run my y2 axis. Has to be a config issue as i tested all 5 axis outputs individually and they all work. I have a 5k investment sitting completed and i cant use it, very frustrating. When i hit home all it racks my gantry(Y1,Y2) ie: only Y1 actually moves, i moved it close to home so it doesn't damage anything but it will not run the other y2, it will work if i wire y1 and y2 in parallel together but i don't want that. I want to be able to autosquare my table when i home.

I have a 4 joint 3 axis machine setup as XYYZ with a mesa 7i96 card, and i cannot get my Y2 joint to run at all whether jogging or in tandem with the other joint. I thought that the output on my Mesa card may be bad so i moved to the #4 output and changed config to match and same thing. I wired the Y1 and Y2 joints in parallel and it works like it should, however that's not the way i built the table to work i have home and limit switches setup for every joint so i can auto square my gantry when homing. I have attached my hal and ini files here. Any help here would be greatly appreciated.

I just wanted to chime in and say I understand your frustration but you're close. You'll get there, don't give up!

I'm not the guy to diagnose a problem with your configs. Shot in the dark here, could it be a problem with your y2 limit switch?

This looks wrong:

setp hm2_7i96.0.stepgen.02.step.invert_output true

I have checked all inputs on the table multiple times, i originally thought that too so i checked again but if it was made it wouldn't try to run to home in linuxcnc itself right?

should i uncheck the invert dir box in pncconf and just wire it reverse?