Got the trans all back together today and it all works. Well it does now, after I worked out that some how, a gear and spline was fitted upside down. Next job is to paint it and bolt it to the chassis.
Where I worked we bought a big ultra sonic cleaner. By big I mean very big. Superb piece of kit but to big for us lads. 12 - 14ft long. The solution was water with 10% caustic acid.