Controlling 64 stepper motors with arduino
I will preset a differnet approach that i would use if i where you:

1- Use a SPI or I2C based stepper motor driver like NCV70521 , L6470 , DRV8811 or similar ICs , this will save you from writing the commutation software for the stepper motor ( if micro-stepping is needed ) . These also work in full and half step mode.

2- Focus on the protocol of communication : 

a- if SPI is choosen (easiest , but you will require 64 pins (chip select) , offcourse you could you decoders / demultiplexer and similar logic ICs to derease the number of needed pins from the microcontroller.

b- if I2C is choosen , then 2 pins of the microcontroller are enough to control all these motors ( SDA and SCL ) but you have to configure different address for each driver.

the advantage of this mode is that the speed or steps are send serially as commands. In your approach you might face some problems in speed , if want to toggle pins at high speed arduino digitalWrite might not be suffcient.