Thanks for those thoughts Robin, pretty much mirrors what I had in mind. Have got an example interrupt procedure for the ARM/Pi so will have a go at rewriting/compiling/installing that tonight and driving it from the pulse generator output of the scope.

Working on ideas for two parallel solutions, one that does it all in software and one that uses a low cost external 'intelligent buffer' (a PIC Micro and not much else... ). I hope that the final solution can work transparently with either, the hardware solution handling higher step rates (>15000 steps/sec would be the likely x-over target) for a relatively low cost plug-in board.