A week on and spare time now permits the process of clean-up the O/Ps with a few 74HC14s, It ain't gonna be petty but at least the waveforms, both inbound and outbound, are gonna be sharp. With a bit of care I will retain the complete opto-isolation on the BoB. Elimination of the now un-necessary optos at the front end of the single axis TB6560 will follow blow by blow.
I think it's fair to say "although any CNC electronics system is a series of steps it needs to be integrated as whole to get the performance expected"
The overall plan continues to be to derive the PC side supply from a spare HDD power connector within the PC. The O/P side of the BoB will come from the 5v rail of the homebrew smorgasbord driver PSU. Or have I got it totally wrong?