Check the area that had the damaged parts. There are numerous limit switches and sense switches that provide signals to the power top module. Maybe a switch is missing, mislocated, broken wiring and is causing a problem. Look for wiring cables in the affected area. Compare the undamaged side to the damaged side and see if you notice anomalies.. . . Now to the actual problem, clearing any codes, sequence issues or getting the hydraulics to operate and get pressure back to complete the operation cycle where it originally stopped. It now warns Top in Operation then is followed by Convertible Top Malfunction. after it stopped in the top down cycle, the top sagged, hyd. motor etc., and I propped it open while it was worked on and so I could access the panel.
I'm after any ideas on how to re-sequence this or clear the fault which may let it continue working? . . . .

I am sure there are body diagnostic codes stored in the power top module. It would be very helpful if you could retrieve any diagnostic codes associated with the power top mechanism. You will need a more robust scan tool (not just one that reads engine management codes / Pxxxx codes.