MACH 3, Warp9 smooth stepper, Leadshine mx4660 Limit switch home switch woes HELP

Hello, I am really new to this but I re built a CNC and I have a few questions that I see crop up on the internet but never any answers. So I hooked up all the gear and have smooth motion, I used the given pins 10 for x,11for y,12 for z,10 slaved to x , 13 for the touchplate probe,15 for the Estop that I am limited to in order to connect to input 1(x),2(y),3(z), and 4(a-slaved to x ). Then I checked the three limit switches and they all function in Mach diagnostics when I trip them. I added 2 more limits in parallel to catch the opposite end of the table. So at this point, I was thinking that if the machine was asked to Ref all home it would gently touch the limit switches and stop but no dice, it goes right through them.

Now if I manually go to the stops, it will trigger the emergency stop, which is great and I assumed that no matter what, if those were touched it would stop the machine from continuing but clearly not.
My questions are:

1- I thought that Leadshines driver would be stopped no matter what if a limit switch is tripped, is there a way to achieve this ? Do people add hard limit switches into the E stop switch to make 100% sure it won't continue to run past the limit switches. I was told somewhere that is something you want to achieve so if the software glitches it will stop the drives at the drive controller so a data link interruption or glitch cannot accidentally allow the motors to crash.

2- what is the safest way to configure the port, pins for what I have ? Should I check the enable for limit x+ x- and home or ?

3- I want to use softlimits so for the softlimits - is there ever a negative number to size the table area. I inputed 50" x 50" and then my x axis started travelling the wrong way on the joystick once I left the soft limit screen. I had checked the home negative box at this point. Once I unchecked that and ran a negative number, it ran the correct direction.

4- Does anyone know why the MX4660 says it has all these input but you get limited to only those listed above ? I mean I wanted to wire my additional x and y limit switches separately but the program limits me to only those ports in MACH3.

5- how do you tell the unit which axis is x- or x+ etc so it knows where it is? I read you can set up the speed and sequence of the homing sequence.

6- I see in the leadshine literature that you need a separate BOB to access the other pins 1,2,3,4,5,6 etc.. once you get one of those, how hard are those to integrate. I'd sure like to add those limits separately and add some home switches.

I know there are a lot of questions here but i've done a lot of digging and it seems the way mine is functioning isn't matching what I see in videos.. I probably have some functions not enabled correctly but the whole direction and which limit is which is a spot I haven't seen anywhere in the program but is something I really need to figure out, that and the speed at which is searches for limit switches, it's travelling way to fast even at 10% on the main screen, it moves too quickly. I have hit the end of travel too many times and I am super scared I am going to break the machine. We catch it instantly each time but still.. it sucks.

Extremely appreciate of any help you people can pass along. :-)

Sincerely, Michael R