I reused my connectors but got new pins. They were JST connectors, the NH series. Here is the part # for the pins alone. SHF-001T-0.8 BS. If you call JST they will send you 24 or so for free as samples if you ask nicely ;-)
I never had the spindle connected to the G540. I just ran it manually( the spindle not the mill). There really isnt a reason to either. You wont be leaving it unattended. I suspect you are correct in the way it is activated. Judging from the manual/auto switch.
Personally I would rewire the steppers if I kept them. I built a belt drive in my lathe to get rid of the geared system it uses.