The PMDX-126 will allow you to use pins 1 and 16 as step and direction, so long as you do not need these pins for other functions on the board such as a PMDX-107 or the K1 relay. If you use pin 1, it is desirable to remove the jumper at JP1 so the relay does not try to follow the signal.
The E-Stop is a harder problem. The PMDX-126 will act internally to kill outputs if you remove the normally closed connection on that input. You can provide an input on pin 15 to signal E-Stop to the Mesa card. The PMDX-126 will treat it as an ordinary signal. If you have two contact sets on your E-Stop switch and use the other set to provide a "relay logic" safety circuit, then things should be OK.
You can use either a PMDX-411 or a PMDX-410 to run your PMDX-126/107 combo under Mach4. Too many choices. Sorry about that. 8-)