Roger,
You will have to strip your motor,you will need to manufacture a bush to weld to the left hand case inside or outside to support the gearstick shaft and the bush will need to include a recess to house a gearstick seal for the lhs case.
As for lining up the shaft ,the existing hole(where the rhs gearstick stub goes into) on the rhs case would be the best guide.you would have to drill it out,and continue it through to the other sidecase to get the correct alignment.
I am not sure if you need to weld a bush to the inside of the rhs case to hold the O ring on the new long gearstick shaft that stops oil transfer between the clutch and gearbox.
The conversion you are attempting is fairly easy for someone with the right equipment.It needs the engine pulled apart to make sure the points mentioned above happen and every everything lines up correctly,otherwise you could end up with a set of cases in the bin.
