How do you home the a axis then or how do you reference your tool
Say you left it on tool 6
Next time you use it it would think tool 6 is the master tool (yes or no ) please advise

the a axis Needs not to be homed, because it is only doing incremental moves.

to remember the tool (witch is in front when you shut down the machine),

Config -> General Config -> right down Corner ->Tool Selection Pesistent

or just enter the tool number in main Screen by Keyboard.


About your spindle Speed:
do you have some more Information how your spindle is connected to mach3 ?

Thomas