Will try to make this as short as possible

I have a Shapeoko XXL and added a new, more robust Z axis. Not being able to use Carbide Motion anymore, I am now using Universal G Code Sender. Everything has gone very smooth with the addition of the new axis, but I have one strange thing going on.

When I home, it goes to the back right corner like always, but now X+ and Y+ go to the right and back. Meaning if I want to move to the front left to set zero's there and start the job I am in negative coordinate numbers. All of the Gcode in jobs that I have created are in positive numbers. So, when I start a job it immediately errors out and tells me I am out of my limits. I have gone through the settings for GRBL, but I'm still having trouble finding the correct settings to correct this.

I have added the settings for my machine here. I tried changing $3=3, but that just made it try to home to the back left.
Hopefully someone here knows what I'm talking about and can help.

Thanks!!
$0=10

$1=255
$2=0
$3=2
$4=0
$5=0
$6=0
$10=255
$11=0.020
$12=0.010
$13=0
$20=1
$21=1
$22=1
$23=0
$24=100.000
$25=2000.000
$26=25
$27=5.000
$30=1000
$31=0
$32=0
$100=40.000
$101=40.000
$102=320.000
$110=5000.000
$111=5000.000
$112=1000.000
$120=320.000
$121=400.000
$122=200.000
$130=889.000
$131=437.000
$132=150.000