i had the same issue... sporadically... since you took yours out... help? i took the clutch actuator out, connector was brittle so the tabs broke off, had to get a piece of wood and tap it off... like a jackass i didn't notice which was it went in and doesn't appear to be one way. mine has rivets not screws, so put grease in the 'boot' hole. just tested it and it's making thunking noises, one of two things. either i put the connector on backwards, so would appreciate if you could tell which colour wire should go to the 1 and 6 (they are numbered in the clutch itself), and did you have to push it towards the 'plunger' to get the wear marks to line up, or just set it in and tighten? i used a reverse clamp to sort of push the body so the wear marks would line up.

Computer controls the speed in which the actuator comes out & goes back in. It meters the distance when starting off in 1st gear in relation to how far the gas pedal is pushed to the floor. Best to remove actuator when full retracted back into housing. The computer reads the position off the drive motor. As long as to not turn the drive motor when removed from actuator body, there should be no issue to remove it & add some grease.

Actuator was in the extend position when unplugged it. Plug motor back into car & put in neutral to return motor to retracted position, same as actuator body. Im not sure though if the spring turns the motor back or if the motor turns itself back

Not sure what you mean? The motor on the clutch actuator could be worn out & weak. Reason for the trouble, just worn out (overheated). Shifting of the gears is also done by electric actuator. Could change the transmission oil & see if it loosens up the shifting or maybe the clutch actuator, shift selenoid/actuator is just getting tired.