Perhaps make the code for the paste just engraving and link the paste feed to the Z-axis direction pin? Have it so if the Z axis is moving down the pin will be high, so the paste switches on, and vice versa. Mach3 latches the direction pins, so it should stay on until the 'tool' is retracted. Might be awkward at the beginning and ends, but a bit of fiddling with the distances and feedrate should sort that? You could link it to coolant / mist or something, but then you've got to find a way to add those commands into the Gcode ... to be fair find and replace + notepad (find Z moves) should be sufficient.

To get a suitable line on each pad select them and contour inside half the width of the pad. Should be feasible as I doubt there's many different size pads.

I've often wondered if you could attach a soldering iron (just the heater+tip) to the router and get it to solder accurately...