Today I rechecked the motor and gearbox on the centre axle with all the other axles in place. Sadly, it was as I feared, the tight fit of the motor in the boiler area pushed the compensation beam down and left the chassis rocking on the centre axle. So back to plan A fitting it on the rear axle and cutting into/the brake cross beam.
Before doing anything drastic I took time out to knock up some ashpan sides and they have cured the gearbox visibility issue.
That still left the gear touching the brake cross beam so I bit the bullet and cut a section out of it.