Electronic – Alternative to A4988 stepper motor driver

I'm not sure what you mean by 'the limit setting potentiometer', but (assuming that you mean the current sense resistors \$R_{S1}\$ and \$R_{S2}\$ (which would be an interesting design, those should be matched low-impedance resistors) I read on page 9, in the section Internal PWM Current Control:

The maximum value of current limiting is set by the selection of RSx and the voltage at the VREF pin. The transconductance function is approximated by the maximum value of current limiting, \$I_{TripMAX}\$ (A), which is set by

\$ I_{TripMAX} = V_{REF} / ( 8 R_S) \$

where \$R_S\$ is the resistance of the sense resistor (Ω) and V_{REF} is the input voltage on the REF pin (V).

Do you have access to the REF pin (pin 17)? If so, adjusting this with a DAC will produce the same effect as varying the sense resistors.

If not, the Enable input is probably a better choice than cutting the power or using the sleep or shut-down pins, those would incur a 1 ms delay (per the description on p. 10).

Yes. Back to back series zeners will work OK. Ensure voltage rating of any one zener is at least slightly greater than maximum voltage that will occur across windings. Note that if you have a centre tapped winding (or motor coil) and the CT is connected to V+ and you ground one end, the other end will rise to +2V+ - so using clamp diodes direct to 1 x V+ will badly affect motor operation.

Another solution is diode from each motor terminal to a voltage sink that is slightly higher than the allowed maximum voltage in normal use. The sink may be a formal power supply with enough load to absorb the spikes or a common zener or clamp regulator which is diode connected from each winding.

You may have to implement a below ground clamp as well depending on circuitry.