With the pokeys you don't realy do a lot if it is working as intended in pokeys config what is not to be relied on it is just a guide.
When you first boot up Mach4 just go through the steps it say to do in the config then ounces that is done reboot mach 4 and the pokeys board. then when you start mach 4 again confirm the pokeys board then just look at the settings to make sure they are correct if not go into the pokeys config to change it there, and restart mach 4 and the pokeys between big setting changes. you have to be careful when setting up any of the pokeys boards that you do not change anything for a start in mach 4 the pokeys does most of it for you.
The first time I set up a 57cnc it took a week of doing the wrong thing then an hour reinstalling mach 4 then letting pokeys set mach 4 up, it is the same with mach3.
You may need to start again.