A bit of progress with the build, I cut down the cross tubes on the seat post from 4" to 3" to allow the standard Scout rear engine plates to slide back and down into the frame. With the lower rails slightly spread to give some clearance, the bottom of the sump now sits level with the underside of the frame rails.
From the outset, I had hoped to keep the seat post intact but this would mean sitting the BSA gearbox further back than I would like and the motor would not sit centrally in the V of the front frame section. If the motor sits 0.5" further back it sits just right, if the gearbox is moved forward 2" it will sit at the same distance as the standard Scout box. With a bit of modification to the inner primary I can get the BSA box to work with an Indian primary case ... Similar to this set up for sale on Ziggy's site using a Triumph ( I think) gearbox
To do this the seat post will need trimmed below the top cross tube and a gearbox mount plate welded in to replace the lower half