Yes, The manuals could be written much better.
Once the Z3 and Z4 numbers are set, never change them manually- always let the machine configure them. If your post outputs those codes, delete them.
Z1 is the critical number for standard taper cutting and Z1 & Z5 are needed for 4 axis. there are a few rare programming options when Z5 will be used (other than graphically) during standard tapering.
PM me if you have more questions. I'm reasonably familiar with the Mits WEDMs.