Just an update. I've found that everything is settling and the internal dome metal drive ring started rubbing against the lower wooden ring and worse still, against the plate the motor is mounted on.
To fix this I simply put some washers under the L brackets mounting the support wheels. This in turn lifted the drive track in relation to the drive cog and in places stressed the glue enough to force it to come loose.
I simply went around the track and epoxied the track back down where it had come loose. I originally used contact adhesive to secure the track
Right now it is running better than ever, pointing out of the dome is quite accurate across the whole sky, so long as I don't use a SBS setup.
Time to consider a motorized shutter