make the second capacitor in the pump 10uf too (from 47uf).
You have connected pull down resistors in the inputs, if you turn power on this way you will activate all four mosfets and you will burn them, A and B are active with gnd and off with positive, you have inverted operation.
The pull down resistors should be changed to pull up (connect them to positive voltage) because a pull down keeps the mosfets always on.
Use a higher value like 47k, the first reason is to use less current, the second is the divider it creates with the input resistor 1K, if you use 1K resistor then when you apply 0v then the transistor base will get Vpullup * (1k/2k).
You have three options:
A) connect a 47k resistor from each input A,B to the +12v, any mcu connected to A shouldn't have a problem with the 12v because of the high resistor value.
B) use a voltage divider, connect one 27k resistor from A to +12 and a 10K resistor from A to gnd (the same for B), this will keep the input to about 3.3v (1/4 divider) when A or B are floating
C) use one additional transistor in eack input A and B to invert the input signal, in this case the new input will be off with gnd so you can use a pull down with a value of about 22k-47k
P.S. you can use one voltage pump for both sides, it is up to you.
Alex