According to the schematic, the M-relay will stay engaged through completed circuits associated with the following switches: a NC ON ADD 100K sw, a NO S-relay switch, a NO E-relay switch, and a few others associated with the N-relay/10K stepper.
Check to see that the NC ON ADD 100K switch is opening when the 100 K stepper steps (it should be on the back of the stepper). If that is OK, then is the associated NO S-relay switch open (S-relay should be disengaged)? I don’t think the associated E-relay and N-relay/10K stepper switches are to blame, but could be worth inspecting too if the NC ONN ADD 100K or NO S-relay switches are fine.
And in terms of the 10K stepper problem, you didn’t upload a photo. It sounds though that your 10K stepper has both right and left hand side switches that are actuated by the actuator arm. Steppers like this that I have seen usually have an extension on the actuator arm that engages switches on one side. I have had a stepper like this in which the extension had broken off the arm and so did what it sounds like you did and moved the switches around so that they could open/close properly when the stepper steps. As long as they’re opening/closing properly, you should be good to go.