Speeds and feeds deep drilling

[JAZZCNC]

Mach3 settings
Steps per x 323.31 velocity x663.6 accel 77.708 step pulse x5 stepdir 5

Your missing steps are not likely to be from cutting or drilling with wrong settings given the slow feeds you were using and the fact the head is so easy to move.
Much more likely to be dropped pulses from either incorrect setup or poor parallel port.

I see one potential cause so first Change the Step pulse=0 Dir= 5 and your missing steps may come back.

Check the Kernal speed. If it's above 25K then drop to 25K and retune motors, you must retune motors.!!.
Mach works best at 25K and the only reason to go higher is if you can't achieve the speeds you require and even then above 45K isn't advised unless very fast and stable PC.
For your machine it doesn't need high Kernal speed and using at higher speeds will potentially make the system unstable.

The steps per are bit Odd number at 323.31 and the number indicates micro stepping around 1600 with 5mm pitch screw which if your parallel port is struggling would put it under stress enough to drop steps.
Consider dropping to 800 micro steps so the PP and PC are not working so hard.!. . Again you must retune the motors.

First check Kernel speed and change if above 25K then change Step/Dir pulse then retune motors. IF kernel Ok then change Step/Dir and try again before changing any thing else.