You are correct. There are three switches on the front of the quill. The top one is a fairly accuarte switch that stops upward motion. the switch just below it is the decel switch. It should make .200 inches before the top stop switch. If it does not, you will have mispositioning issues. Trust me. Bottom most switch is a overtravel limit switch. It is a normally closed switch, wired in series with the rest of the overtravel switches. Thus any one of these switches can shut the drives off by breaking open the string.
What is the AC voltage of the Z axis feed coming from T2 in the top of the back electrical cabinet? IE: wires 11 and 12 are the X axis, 13 and 14 are the Y and thus 15 and 16 must be the Z. I am doing this from memory. If it is greater than 64 VAC, you will blow transistors like candy. The only way to bring this down is to lower the power coming into the machine. What is the voltage coming in?
You did not mention which BOSS version this is. I wonder if it has the small SMS board. It is meant to try and limit transistor blowing when an axis is moving and it hits a limit switch or someone pushes the emergency stop switch.
Are you using 2N6547 transistors?
Is the static current set to 8 amps DC? Note never attach or remove a meter unless drives are off.
Are the DC axis fuses of the screw in variety? NOT good if so.
Well, that is a start.