It would be nice to see some pics of the machines.What you do next it seems to me depends on your level of comfortability & expertise.
It seems the machine is basically working-that is a great sign. Those areas of concern eg pin reset I would attempt one at a time so you do not create additional issues. Do you have a schematic to facilitate your diagnosis of issues. Finally Clay Hurrells' big ball bowler DVD is a great resource on 'fixing' a ball bowler.