So heres a pic of one side of all the gears, on the left the gears and 2 shafts taken from a plunger "semi unit" box, the gears are marked with V16 albeit some markings are incomplete. On the right are gears and shafts taken from a 56 swing arm box most of which are marked EN36. The far left has the layshaft gears from the plunger box. I've shown just the "dog" side of the gears as the other sides all appear identical.
So the visual differences are:
1. The layshafts have the wire spring clip in different places on the shaft, this means the gear kept in place by the clip will not fit on both layshafts. The inside of the gears dogs are machined away on the plunger gear to allow the gear to slide further over the clip. My guess is the s/a design is stronger as more gear engages with the hex shaft. Without trying it I would say the plunger layshaft and that gear would fit into a s/a box, if one really needed to use that gear, but see below ref lube provision for the plunger layshaft. There's a close pic of the end of the shafts showing the difference (pic 227), also a close up of the inside of the 2 different gears (pic 224).
2. The plunger layshaft does not have a spiral groove for the drive side bush. The bush also does not spiral groove either box, I guess the groove on the s/a shaft is to improve the life of the bearing, the bush in the plunger box has a longitudenal slot I guess in place of a spiral on the shaft. the s/a bush does not have this cutaway.
3. The dogs are different on two of the plunger gears, the m/s gear next to the sleeve gear, and the l/s bottom gear. There's a pic of the bottom gear in an earlier post and the other gear from each box are in pics below (pic 225 and 226). My guess is these changes in design are to increase strength rather than gear changing but I could be wrong, the design change did not appear to require a change in design of the gear the dogs engage with (this assumes the boxes I a have contain original gears of course!).
4. The washers on the layshaft are of different thickness, though I'm not sure if that is caused by wear, or to get the end float correct.
Anyway, I hope all these posts that adds to the forum knowledge and helps someone.
My problem (edit: now all answered/solved thanks all) has now switched from being whether to use a V16 bottom gear in a s/a box (it is has slightly different dog design to the EN36 gear) to sourcing a new mainshaft (or maybe I'll use the plunger mainshaft and spend the money on a better clutch instead).