Took me more than 10 mins as I was being thorough.
Sketch now reads
//////////////////// *********** Motor drive connections **************
//Connect ground only for cytron, Connect Ground and +5v for IBT2
//Dir1 for Cytron Dir, Both L and R enable for IBT2
#define DIR1_RL_ENABLE 4 //PD4
//PWM1 for Cytron PWM, Left PWM for IBT2
#define PWM1_LPWM 9 //PD9
///////////////////////////////////////////////////////////////////////////////////////
I’ve attached GND - GND
PWM to PD9
DIR to PD4
Using autosteer below, I am seeing 0.01v on PD9, same as I got on PD3.
To be sure, I checked the 5v and 3.3v output pins and they read 5v and 3.3v respectively so the multimeter is working.