Setting up a machine without a Z Axis

I'm converting over an old Koike Oxy Fuel table that has a Burny controller on it to run on Qtplasmac. Swapped out all the electronics. Can move the axes around how I want and it'll run whatever shape I program. However a few issues in running into, probably just me overlooking ini file settings.
1. The torch won't activate at all when the program is running. The torch only works when I manually hit the "Torch Pulse" button. 
2. I have a manually controlled Z Axis, no need for that auto height stuff on Oxy Fuel cause the height not being right is more forgiving. But the problem I run into is when I go to run a program without homing, it follows the path it should, but when I do home it goes to cut the shape and then the Z Axis starts moving on the screen and it throws the error "bottom limit reached while probing down". I feel like there's some simple solution that might fix both of these problems that I'm just not seeing. 
3. Also a third random question while I'm here, I know I can set various pierce times for different materials but it's there a way to force the machine into always manually piercing, like a M1. But in the parameters/in, I that itll pause and make me hit like cycle start or something to do the pierce. Cause while I can let it run auto, pierce times are more finicky with oxy fuel and it can vary day to day and plate to plate.