I’m having trouble with not cutting thru all over. Like something isn’t zeroed our right. I’ve done with probe and I’ve done it manually. It’s off .04 from front to back on my table
You will need to trim your table surface so that it is parallel to the movement of the axes. I have the same problem. I attach a piece of wood with double sided tape to my plywood table and then surface it with a 1/2" router bit. I have a 750 x 1000 machine, so I only do it to the area I’m working on. Eventually I’ll need to come up with another plan with a completely trammed surface.
Your spoil board need tweaking or surface skimming, never assume its uniform in thickness nor parallell to Z-height.
Once the surface is truly flat (relative to Z) I suggest you use the spoil board Z as reference. Find its zero, jog up the material thickness + a little extra. Use this level as your Z zero and set total cut depth = material thickness + whatever little extra you added.