I think you can make this work without the I/O expander:
Move Motor Enable from D6 to D5
Move PWM from A6 to D6
Move Encoder Interrupt 4 from D5 to A6.
You still may have some trouble though because of this:
// D0-D3 were initially chosen, but because
// individual control of dis/en'abling their
// interrupt handlers was not available, A6, A7
// D3 and D4 were chosen instead. D0, D1, D2
// A0, A1, A3, A4 are all tied to one interrupt
// handler
So, because you really need A7 as well... you'd have to find another PWM from the Analog pins, because you are using the I2C/PWM pins already for I2C. Perhaps you could get a I2C to PWM chip to generate your PWM, like this one: Adafruit 16-Channel 12-bit PWM/Servo Driver - I2C interface [PCA9685] : ID 815 : $14.95 : Adafruit Industries, Unique & fun DIY electronics and kits